Nucleotide sequences in bacteriophage ribonucleic acid. The eighth hopkins memorial lecture

An RNA Phage Lab: MS2 in Walter Fiers' laboratory of molecular biology in Ghent, from genetic code to gene and genome, 1963-1976

The importance of viruses as model organisms is well-established in molecular biology and Max Delbrück's phage group set standards in the DNA phage field. In this paper, I argue that RNA phages, discovered in the 1960s, were also instrumental in the making of molecular biology. As part of experimental systems, RNA phages stood for messenger RNA (mRNA), genes and genome. RNA was thought to mediate information transfers between DNA and proteins. Furthermore, RNA was more manageable at the bench than DNA due to the availability of specific RNases, enzymes used as chemical tools to analyse RNA. Finally, RNA phages provided scientists with a pure source of mRNA to investigate the genetic code, genes and even a genome sequence. This paper focuses on Walter Fiers' laboratory at Ghent University (Belgium) and their work on the RNA phage MS2. When setting up his Laboratory of Molecular Biology, Fiers planned a comprehensive study of the virus with a strong emphasis on the issue of structure. In his lab, RNA sequencing, now a little-known technique, evolved gradually from a means to solve the genetic code, to a tool for completing the first genome sequence. Thus, I follow the research pathway of Fiers and his 'RNA phage lab' with their evolving experimental system from 1960 to the late 1970s. This study illuminates two decisive shifts in post-war biology: the emergence of molecular biology as a discipline in the 1960s in Europe and of genomics in the 1990s.

Characterization of the regulatory region of Adra2c, the gene encoding the murine alpha2C adrenoceptor subtype

The 5' flanking sequence (3,227 base pairs, bp) of the mouse Adra2c subtype gene was determined and characterized. The transcription start site was mapped to nucleotide 'A' of two initiator motifs in tandem array, i.e. 1,159 and 1,153 bp upstream from the initiation codon of the open reading frame (ORF) of Adra2c, respectively. One structural feature salient to the 5' regulatory region of Adra2c is present in the sequence 1 kb immediately upstream from the receptor ORF, which is highly enriched in GC content (76%) and CpG island counts (i.e. CpG/GpC, 146:177), and thus rich in Sp1-binding motifs. At the 3' flanking region, the polyadenylation signal was mapped to 481 bp downstream from the termination codon. The transcript defined by sequence data thereby is consistent with a size of 3 kb (brain form) determined by Northern blot analysis. The transgene, Adra2c-NN- lacZ, which links the promoter region of Adra2c to the lacZ reporter gene, was constructed in order to evaluate the functional capacity of the promoter and the putative motifs residing within the defined regulatory region (1.9 kb upstream from the ORF) in directing the reporter gene expression in vitro in transiently transfected cells and in vivo in transgenic (Tg) mice. Permissive cell types to Adra2c-NN include those derived from neural and kidney lineages. Significant Adra2c-NN-driven reporter expression in Tg mice established suggests that alpha2C adrenoceptor expression is permissive under Adra2c-NN in central (cerebral cortex, hippocampus, subthalamus, hypothalamus, superior colliculus, cerebellum, and brain stem) and peripheral (pancreatic beta-islets) tissues.

Studies on sheep kidney nuclease. I. An improved purification method and some properties

An improved purification method of the sheep kidney nuclease (nuclease SK) specific for single-strans nucleic acid, which includes extraction with 0.85% NaCl, treatment with DEAE-cellulose, fractionation with polyethylene glycol, phospho-cellulose chromatography, CM-Sephadex chromatography and phospho-cellulose rechromatography is described. The nuclease was purified approx. 390-fold. Identity was established by comparison with known properties. Molecular weight was estimated to be 52 000-53 000 by gel filtration on Sephadex G-100. The properties of the purified enzyme agreed well those reported previously. The purified enzyme hydrolyzed heat-denatured calf thymus DNA, yeast RNA and no hydrolytic activity for native calf thymus DNA, A2'-pA, A3'-pA, ADP, ATP, 5'-AMP and cyclic AMP.

The occurrence in amino acid sequences of extensive informational symmetries based on possible codon-codon complementarity in the encoding polynucleotides

1. A procedure is described for the detection and assessment of informational complementarity in an amino acid sequence; it is based on possible autocomplementarity in the mRNA, and involves codon-to-codon matching. 2. This procedure was applied to myelin basic protein, a variety of protamines, histone IV, silk fibroin, rat skin collagen alpha1 chain and a sheep keratin. A multiplicity of extensive low-probability informational symmetries, based on codon-to-codon matching, were detected. 3. These low-probability orderings, which are independent of the actual mRNA codons, are rationalized in terms of the evolutionary ordering of the amino acid sequences concerned, in such a way that constraints on the secondary structure of the coding polynucleotides were satisfied. This possible interpretation is supported by a number of significant common properties of the protein sequences analysed.

The Croonian Lecture, 1975. Nucleotide sequences in DNA

DNA, the chemical component of the gene, plays a central role in biology and contains the whole information for the development of an organism, coded in the form of sequences of the four nucleotide residues. The lecture describes the development and application of some methods that can be employed to deduce sequences in these very large molecules. Special attention has been applied to a rapid simple method in which DNA polymerase is primed with specific oligonucleotide primers, thus making it possible to study small sections of radioactively labelled DNA. The techniques have been applied to the single-stranded DNA of bacteriophage ϕ X 174, and two sequences of about 250 nucleotides long have been deduced and related to the amino acid sequences of the proteins for which they code.

A sequence of seventy-three nucleotides from the coliphage R17 genome

1. A sequence of 73 nucleotides of the RNA genome from coliphage R17 was determined. It can be read through in only one translational frame. The fragment is not part of the coatprotein cistron (Min Jou et al., 1972), nor does it come from the untranslated sequences described previously (Steitz, 1969; Nichols, 1970; Cory et al., 1970; de Wachter et al., 1971; Contreras et al., 1971; Cory et al., 1972). It contains two sequences of 23 and 24 nucleotides, 22 of which are identical. This kind of reiteration is the first one found in bacteriophage nucleic acid. 2. Improved conditions were found and tested for blocking oligonucleotides with carbodi-imide and cleaving by ribonuclease A at cytidylate residues. 3. A synthetic medium is described which allows labelling in vivo with (32)P to give specific radioactivities higher than those obtained in the procedures used previously.

Nucleotide sequences of two fragments from the coat-protein cistron of bacteriophage R17 ribonucleic acid

Bacteriophage R17 RNA was labelled with (32)P and was subjected to partial digestion with ribonuclease T(1). The products were fractionated by ionophoresis on polyacrylamide gel. Two fragments were purified and their nucleotide sequences determined by methods involving complete and further partial digestion with ribonucleases A and T(1). Fragment 20 had a sequence that coded for the amino acids in positions 32-53 of the coat protein of the bacteriophage. Fragment 20X, on further purification in 7m-urea, gave rise to two smaller nucleotides whose sequences coded for the amino acids in positions 56-66 and 67-76 of the coat protein. The sequence of the two fragments was such that they could be written in the form of loops stabilized by base-pairing.

Assay for secondary structure in ribonucleic acid

A chromatographic procedure is described which can discriminate among single-stranded ribonucleic acid (RNA) molecules in solution on the basis of the extent of their secondary structure. The assay is effected through chromatography at different temperatures with columns of cellulose CF-11. When Sindbis virus RNA is chromatographed in this system, the ratio of the amounts of RNA eluting in the single-stranded peak to those eluting in the double-stranded peak increases at higher temperatures, presumably a measure of the relative amounts of Sindbis virus RNA secondary structure at different temperatures. With this assay, Sindbis virus RNA, phage f2 RNA, and polyuridylate have been found to have different amounts of secondary structure.

Messenger RNA structure: compatibility of hairpin loops with protein sequence

Examination of the amino acid sequences of human cytochrome c and the alpha-chain variant of human hemoglobin Constant Spring has revealed the possiblity for base-paired hairpin loops in the messenger RNA's for these proteins. A similar analysis of the bacteriophage R17 coat protein suggests an additional unobserved loop in the R17 RNA. If such loops are present in messenger RNA's generally, it would suggest that DNA has more than one stable base-paired conformation.