Yeast suppressors of UAA and UAG nonsense codons work efficiently in vitro via tRNA

Translational recoding signals: Expanding the synthetic biology toolbox

Innovation follows discovery. If the 20th century was a golden age of discovery in the biomolecular biosciences, the current century may be remembered by the explosion of beneficial devices and therapies conceived by the bioengineers of the era. Much as the development of solid-state electronic components made possible the information revolution, the rational combining of millions of basic molecular control modules will enable the development of highly sophisticated biomachines that will make today's smartphones appear rudimentary. The molecular toolbox is already well-stocked, particularly in our ability to manipulate DNA, control transcription, generate functionally novel hybrid proteins, and expand the genetic code to include unnatural amino acids. This review focuses on how RNA-based regulatory modules that direct alternative readings of the genetic code can be employed as basic circuit components to expand our ability to control gene expression.

Comprehensive survey of condition-specific reproductive isolation reveals genetic incompatibility in yeast

Genetic variation within a species could cause negative epistasis leading to reduced hybrid fitness and post-zygotic reproductive isolation. Recent studies in yeasts revealed chromosomal rearrangements as a major mechanism dampening intraspecific hybrid fertility on rich media. Here, by analysing a large number of Saccharomyces cerevisiae crosses on different culture conditions, we show environment-specific genetic incompatibility segregates readily within yeast and contributes to reproductive isolation. Over 24% (117 out of 481) of cases tested show potential epistasis, among which 6.7% (32 out of 481) are severe, with at least 20% of progeny loss on tested conditions. Based on the segregation patterns, we further characterize a two-locus Dobzhansky–Müller incompatibility case leading to offspring respiratory deficiency caused by nonsense mutation in a nuclear-encoding mitochondrial gene and tRNA suppressor. We provide evidence that this precise configuration could be adaptive in fluctuating environments, highlighting the role of ecological selection in the onset of genetic incompatibility and reproductive isolation in yeast.

Chromosomal rearrangements may hamper intraspecific hybrid fertility. Here the authors show that environment-specific genetic incompatibility segregates readily within intermating populations and leads to intrinsic reproductive isolation within a yeast species.

Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element

In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3′-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the ∼150 nt 3′-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem–loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem–loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3′ RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis.

A new method for the isolation of recombinant baculovirus

An improved method for the isolation of baculovirus recombinants is described. The method involves the replication and maintenance of the baculovirus genome in the yeast Saccharomyces cerevisiae which was accomplished by the isolation of a baculovirus recombinant containing yeast ARS and CEN sequences ensuring stable replication in yeast and a URA3 selectable marker. The viral DNA maintained its ability to replicate in insect cells. An efficient and rapid selection system was set up, to isolate viral recombinants in yeast; DNA from selected yeast colonies was transfected into insect cells to obtain recombinant virus. We demonstrate the utility of this system by isolating recombinant viruses that express two different members of the CREB/ATF family of transcription factors.

5S-rRNA genes in rice embryos

The 5S-rRNA from the ungerminated and 48-h-germinated rice embryos differs from the wheat, rye and maize by two nucleotides. The 48-h-germinated embryos contain another species of 5S-rRNA which differs by 3 nucleotides from the ungerminated embryos, thereby showing the expression of two 5S-rRNA genes during germination. The 5S-rRNA genes are present in tandem repeats of a 0.3-kb sequence with some length heterogeneity in the rice genome. The 5S-rRNA gene that was sequenced is identical to that of wheat and maize, except for two nucleotides, C and T, which are interchanged at positions 107 and 117. The insert of continuous 5S-rRNA gene in pBR322 was transcribed in vitro much more efficiently than the discontinuous gene. There was no homology between the 184-bp spacer sequence of 5S-rRNA genes in rice and other systems except the presence of the oligo(T) transcription terminator sequence.

Unusual ciliate-specific codons in Tetrahymena mRNAs are translated correctly in a rabbit reticulocyte lysate supplemented with a subcellular fraction from Tetrahymena

The codon usage of Tetrahymena thermophila and other ciliates deviates from the 'universal genetic code' in that UAA and probably UAG are not translational termination signals but code for glutamine. Therefore, translation in vitro of mRNA from Tetrahymena in a reticulocyte lysate is prematurely terminated if a UAA or UAG triplet is present in the reading frame of the mRNA. We show that the addition of a subcellular fraction from Tetrahymena thermophila enables a rabbit reticulocyte lysate to translate Tetrahymena mRNAs into full-sized proteins. The activity of the subcellular fraction is shown to depend on the combined function of a protein component(s) and a tRNA(s). The subcellular fraction is easily prepared and its usefulness for the identification of isolated mRNAs from Tetrahymena by their translation products in vitro is demonstrated.

Yeast amber suppressors corresponding to tRNA3Leu genes

Amber suppressors previously isolated from the yeast Saccharomyces cerevisiae and belonging to the same phenotypic class (Liebman et al., 1976) were assigned to nine different linkage groups named SUP52 through SUP60. One of these suppressors, SUP52, had been shown to cause the insertion of leucine and had been genetically mapped (Liebman et al., 1977). The following additional amber suppressors were mapped: SUP53 maps near the centromere of chromosome III closely linked to leu2; SUP54 maps on chromosome VII, 6 cM distal to trp5; SUP56 maps on chromosome I, 5.4 cM distal to ade1; SUP57 maps on chromosome VI, closely linked to met10; and SUP58 maps on the left arm of chromosome XI, loosely linked to met14. We show by protein analysis that like SUP52, the suppressors SUP53 through SUP56 are leucine-inserters. Furthermore, by hybridization with a cloned tRNA3Leu probe we demonstrate that at least SUP53, SUP54, SUP55 and SUP56 contain mutations in redundant tRNA3Leu genes because they each generate a new XbaI site in a DNA fragment encompassing a tRNA3Leu gene. These new XbaI sites are predicted by the known sequences of tRNA3Leu genes if the CAA anticodon mutates to the amber suppressing anticodon CTA. It is likely that each of the nine suppressors in this phenotypic class contain similar mutations in different tRNA3Leu genes since we find that there are approximately nine unlinked redundant copies of tRNA3Leu genes in haploid strains.

Resolution of the discrepancy between a gene translation--termination codon and the deduced sequence for release of the encoded polypeptide

The translation-termination codon of the synthetase gene of the RNA phage MS2 has been determined, by nucleotide sequencing and suppression studies in vitro, to be UAG. However in one of the only two studies on the signals for polypeptide chain release at the end of genes, Capecchi and Klein [(1970) Nature (Lond.) 226, 1029-1033] deduced that the synthetase of an almost identical phage, R17, is released at UAA. Here we show that under certain conditions the synthetase is released at the UAG terminator but that this UAG is especially prone to read-through with resulting release at the downstream UAA codon. The possible significance of the UAG being in a context prone to leakiness is discussed but is unresolved.

Uridine-33 in yeast tRNA not essential for amber suppression

The nucleotide at position 33 on the 5' side of the anticodon of almost all tRNAs is a uridine. Crystallographic studies of different tRNAs reveal that although the precise orientation of uridine-33 is not always the same, it connects the anticodon stacked along the 3' side of the loop with the pyrimidine-32 stacked on the 5' side of the loop. The remarkably conserved nature of uridine-33 and its unique position in the anticodon loop structure has led to suggestions that this nucleotide has an essential role in the translational mechanism. We have developed a biochemical procedure to replace nucleotides 33-35 in yeast tRNATyr with any desired sequence and used it to construct amber suppressor tRNAs having different nucleotides at position 33. As all of these synthetic amber suppressor tRNAs functioned well in eukaryotic in vitro suppression assays, we conclude that uridine-33 does not have an obligatory role in the translation mechanism.

The genes sup-7 X and sup-5 III of C. elegans suppress amber nonsense mutations via altered transfer RNA

The sup-5 III and sup-7 X suppressors in C. elegans have previously been shown to have many genetic properties in common with tRNA nonsense suppressors of microorganisms. We report here the results of two lines of investigation into the molecular basis of these suppressors. In one, which sought to determine the nature of suppressible alleles, we demonstrate through DNA sequencing studies that a suppressible allele, unc-54(e 1300) I, of the myosin heavy chain gene contains a C leads to T substitution, which changes a glutamine codon to amber terminator at residue 1903. In the other approach, which sought to define the nature of the suppressing activity, we show through in vitro translation studies that tRNA fractions from the suppressor strains, but not wild-type, promote the specific readthrough of amber terminators of three different messenger RNAs. We conclude that sup-5 and sup-7 result in readthrough of amber terminators in vivo through an altered tRNA.

In vitro nonsense suppression in [psi+] and [psi-] cell-free lysates of Saccharomyces cerevisiae

An homologous in vitro assay for yeast nonsense suppressors was used to examine the effect of the cytoplasmically inherited genetic determinant [psi] on the efficiency of in vitro nonsense suppression. The efficiency of all three types of yeast tRNA-mediated nonsense suppressor (ochre, amber, and UGA) is much greater in cell-free lysates prepared from a sup+ [psi+] strain than in lysates prepared from an isogeneic sup+ [psi-] strain. Lysates prepared from a [psi-] strain, into which the [psi+] determinant was reintroduced by kar1-mediated cytoduction, support efficient suppression. Evidence is also presented that [psi-] lysates contain an inhibitor of in vitro nonsense suppression.

Nonsense suppression in Schizosaccharomyces pombe: the S. pombe Sup3-e tRNASerUGA gene is active in S. cerevisiae

The gene encoding the efficient UGA suppressor sup3-e of Schizosaccharomyces pombe was isolated by in vivo transformation of Saccharomyces cerevisiae UGA mutants with S. pombe sup3-e DNA. DNA from a clone bank of EcoRI fragments from a S. pombe sup3-e strain in the hybrid yeast vector YRp17 was used to transform the S. cerevisiae multiple auxotroph his4-260 leu2-2 trp1-1 to prototrophy. Transformants were isolated at a low frequency; they lost the ability to grow in minimal medium after passaging in non-selective media. This suggested the presence of the suppressor gene on the non-integrative plasmid. Plasmid DNA, isolated from the transformed S. cerevisiae cells and subsequently amplified in E. coli, transformed S. cerevisiae his4-260 leu2-2 trp1-1 to prototrophy. In this way a 2.4 kb S. pombe DNA fragment carrying the sup3-e gene was isolated. Sequence analysis revealed the presence of two tRNA coding regions separated by a spacer of only seven nucleotides. The sup3-e tRNASerUGA tRNA gene is followed by a sequence coding for the initiator tRNAMet. The transformation results demonstrate that the cloned S. pombe UGA suppressor is active in S. cerevisiae UGA mutant strains.

Replacement of anticodon loop nucleotides to produce functional tRNAs: amber suppressors derived from yeast tRNAPhe

The method of anticodon loop replacement has been used to make derivatives of yeast tRNAPhe. By constructing tRNAs with a CUA anticodon, complementary to the amber (UAG) terminator, functional amber suppressor tRNAs were produced. The activity of these tRNAs was assayed in a mammalian cell-free protein synthesizing system. The level of suppression reflects the efficiency of codon recognition. tRNAs were constructed with either A, C, U, or G on the 3' side of the CUA anticodon. The tRNAs containing the purines were efficient amber suppressors, whereas those containing pyrimidines were inefficient.

Establishment of mammalian cell lines containing multiple nonsense mutations and functional suppressor tRNA genes

We describe the generation of mammalian cell lines carrying amber suppressor genes. Nonsense mutants in the herpes simplex virus thymidine kinase (HSV tk) gene, the Escherichia coli xanthine-guanine phosphoribosyl transferase (Eco-gpt) gene and the aminoglycoside 3' phosphotransferase gene of the Tn5 transposon (NPT-II) were isolated and characterized. Each gene was engineered with the appropriate control signals to allow expression in both E. coli and mammalian cells. Expression in E. coli made possible the use of well developed bacterial and phage genetic manipulations to isolate and characterize the nonsense mutants. Once characterized, the nonsense mutants were transferred into mammalian cells by microinjection and used, in turn, to select for amber suppressor genes. Xenopus laevis amber suppressor genes, prepared by site-specific mutagenesis of a normal X. laevis tRNA gene, were microinjected into the above cell lines and selected for the expression of one or more of the amber mutant gene products. The resulting cell lines, containing functional amber suppressor genes, are stable and exhibit normal growth rates.

Endogenous read-through of a UGA termination codon in a Saccharomyces cerevisiae cell-free system: evidence for involvement of both a mitochondrial and a nuclear tRNA

Globin mRNA, translated in a Saccharomyces cerevisiae cell-free protein synthesizing system prepared from a [psi+ rho+] strain, primarily directed the synthesis of alpha- and beta-globin. A third globin mRNA-specific polypeptide was also synthesized, representing approximately 10% of the total translation products. This polypeptide (beta') was synthesized by translational read-through of the beta- globin mRNA UGA terminator and was mediated primarily by an endogenous tRNA coded for by the mitochondria. This mitochondrial tRNA, when charged, could be preferentially bound, in high salt, to benzoylated DEAE-cellulose, a characteristic of a tRNATrp. The synthesis of beta- mediated by this mitochondrial tRNATrp was significantly reduced when the translation system was prepared from an isogenic [psi-] strain. Evidence for a nuclear-coded tRNA, also able to suppress the beta-globin mRNA UGA terminator in [psi+] but not [psi-] lysates, was also obtained. The presence of these endogenous UGA suppressor activities in the yeast cell-free system should allow successful in vitro translation of mitochondrial mRNAs.

Endogenous read-through of a UGA termination codon in a Saccharomyces cerevisiae cell-free system: evidence for involvement of both a mitochondrial and a nuclear tRNA

Globin mRNA, translated in a Saccharomyces cerevisiae cell-free protein synthesizing system prepared from a [psi+ rho+] strain, primarily directed the synthesis of alpha- and beta-globin. A third globin mRNA-specific polypeptide was also synthesized, representing approximately 10% of the total translation products. This polypeptide (beta') was synthesized by translational read-through of the beta- globin mRNA UGA terminator and was mediated primarily by an endogenous tRNA coded for by the mitochondria. This mitochondrial tRNA, when charged, could be preferentially bound, in high salt, to benzoylated DEAE-cellulose, a characteristic of a tRNATrp. The synthesis of beta- mediated by this mitochondrial tRNATrp was significantly reduced when the translation system was prepared from an isogenic [psi-] strain. Evidence for a nuclear-coded tRNA, also able to suppress the beta-globin mRNA UGA terminator in [psi+] but not [psi-] lysates, was also obtained. The presence of these endogenous UGA suppressor activities in the yeast cell-free system should allow successful in vitro translation of mitochondrial mRNAs.

Construction of a functional human suppressor tRNA gene: an approach to gene therapy for beta-thalassaemia

A human tRNALys gene was converted to an amber suppressor by site-specific mutagenesis of the anticodon. The mutated tRNALys gene directed synthesis of a tRNA that suppressed the UAG amber nonsense mutation in beta O thalassemia mRNA. Such genes may be used to detect other nonsense mutations in mammalian cells and may provide an approach to gene therapy for beta O thalassaemia due to nonsense mutations.

Lac4 is the structural gene for beta-galactosidase in Kluyveromyces lactis

Using genetic and biochemical techniques, we have determined that beta-galactosidase in the yeast Kluyveromyces lactis is coded by the LAC4 locus. The following data support this conclusion: (1) mutations in this locus result in levels of beta-galactosidase activity 100-fold lower than levels in uninduced wild type and all other lac- mutants; (2) three of five lac4 mutations are suppressible by an unlinked suppressor whose phenotype suggests that it codes for a nonsense suppressor tRNA; (3) a Lac+ revertant, bearing lac4--14 and this unlinked suppressor, has subnormal levels of beta-galactosidase activity, and the Km for hydrolysis of o-nitrophenyl-beta, D-galactoside and the thermal stability of the enzyme are altered; (4) the level of beta-galactosidase activity per cell is directly proportional to the number of copies of LAC4; (5) analysis of cell-free extracts of strains bearing mutations in LAC4 by two-dimensional acrylamide gel electrophoresis shows that strains bearing lac4--23 and lac4--30 contain an inactive beta-galactosidase whose subunit co-electrophoreses with the wild-type subunit, while no subunit or fragment of the subunit is observable in lac4--8, lac14--14 or lac4--29 mutants; (6) of all lac4 mutants, only those bearing lac4--23 or lac4--30 contain a protein that cross-reacts with anti beta-galactosidase antibody, a finding consistent with the previous result; and (7) beta-galactosidase activity in several Lac+ revertants of strains carrying lac4--23 or lac4--30 has greatly decreased thermostability.

Yeast ochre suppressor SUQ5-ol is an altered tRNA Ser UCA

Ochre suppressor tRNA was partially purified from strains of Saccharomyces cerevisiae containing the serine-inserting class III suppressor SUQ5-ol. RNA sequence analysis of this tRNA indicated that the suppressor is derived from a UCA-decoding tRNA Ser by a G leads to U substitution in the middle position of the anticodon. The suppressor further differs from the wild-type UCA-decoding tRNA Ser in that the mutant anticodon lacks the modified uridine found in the wobble position of the wild-type tRNA and contains instead another modification in or near the anticodon.

Only one of two closely related yeast suppressor tRNA genes contains an intervening sequence

The yeast genes that code for the serine-inserting SUP-RL1 amber and SUQ5 ochre suppressors have been cloned and sequenced. These two unlinked genes differ by only three base pairs in their coding regions yet they encode tRNAs of different translational specificities, and while the SUP-RL1 gene has a 19-base pair intervening sequence, the SUQ5 gene has none.

Nonsense suppression in eukaryotes: the use of the Xenopus oocyte as an in vivo assay system

Amber, ochre, and opal nonsense suppressor tRNAs isolated from yeast were injected into Xenopus laevis oocytes together with purified mRNAs (globin mRNA from rabbit, tobacco mosaic virus-RNA). Yeast opal suppressor tRNA is able to read the UGA stop codon of the rabbit beta-globin mRNA, thus producing a readthrough protein. A large readthrough product is also obtained upon coinjection of yeast amber or ochre suppressor tRNA with TMV-RNA. The amount of readthrough product is dependent on the amount of injected suppressor tRNA. The suppression of the terminator codon of TMV-RNA is not susceptible to Mg++ concentration or polyamine addition. Therefore, the Xenopus laevis oocyte provides a simple, sensitive, and well buffered in vivo screening system for all three types of eukaryotic nonsense suppressor tRNAs.

Suppression of murine retrovirus polypeptide termination: effect of amber suppressor tRNA on the cell-free translation of Rauscher murine leukemia virus, Moloney murine leukemia virus, and Moloney murine sarcoma virus 124 RNA

The effect of suppressor tRNA's on the cell-free translation of several leukemia and sarcoma virus RNAs was examined. Yeast amber suppressor tRNA (amber tRNA) enhanced the synthesis of the Rauscher murine leukemia virus and clone 1 Moloney murine leukemia virus Pr200(gag-pol) polypeptides by 10- to 45-fold, but at the same time depressed the synthesis of Rauscher murine leukemia virus Pr65(gag) and Moloney murine leukemia virus Pr63(gag). Under suppressor-minus conditions, Moloney murine leukemia virus Pr70(gag) was present as a closely spaced doublet. Amber tRNA stimulated the synthesis of the "upper" Moloney murine leukemia virus Pr70(gag) polypeptide. Yeast ochre suppressor tRNA appeared to be ineffective. Quantitative analyses of the kinetics of viral precursor polypeptide accumulation in the presence of amber tRNA showed that during linear protein synthesis, the increase in accumulated Moloney murine leukemia virus Pr200(gag-pol) coincided closely with the molar loss of Pr63(gag). Enhancement of Pr200(gag-pol) and Pr70(gag) by amber tRNA persisted in the presence of pactamycin, a drug which blocks the initiation of protein synthesis, thus arguing for the addition of amino acids to the C terminus of Pr63(gag) as the mechanism behind the amber tRNA effect. Moloney murine sarcoma virus 124 30S RNA was translated into four major polypeptides, Pr63(gag), P42, P38, and P23. In the presence of amber tRNA, a new polypeptide, Pr67(gag), appeared, whereas Pr63(gag) synthesis was decreased. Quantitative estimates indicated that for every 1 mol of Pr67(gag) which appeared, 1 mol of Pr63(gag) was lost.

Recessive nonsense-suppression in yeast Saccharomyces cerevisiae: the study of 80 S ribosomes accumulated in suppressor strain under non-permissive conditions

The shift of recessive suppressor mutant of yeast Saccharomyces cerevisiae from permissive to restrictive conditions is accompanied by polysome decay and accumulation of 80 S ribosomes (Smirnov et al., 1976). In this paper some properties of 80 S ribosomes are studied. It is demonstrated that polysome decay under non-permissive conditions is not the consequence of the impairment of RNA synthesis. More than 70% of 80 S ribosomes accumulated under non-permissive conditions contain bound peptidyl-tRNAs localized in P-ribosomal site. tRNA moiety of bound peptidyl-tRNA is able to accept all 20 natural amino acids after chemical deacylation. Therefore it is not a specific isoacceptor species but rather total tRNA that is bound to ribosomes. The polypeptide residues of these peptidyl-tRNAs are heterogeneous in size. Their molecular weights are comparable with the molecular weights of the completed polypeptides. Some of the 80 S ribosomes accumulated under non-permissive conditions contain poly-A+ RNA. In conclusion, possible mechanism of the impairment of translation under non-permissive conditions in recessive suppressor strain is discussed.

A UGA termination suppression tRNATrp active in rabbit reticulocytes

A tRNATrp was purified from rabbit reticulocytes which suppresses the UGA termination codon of beta-haemoglobin mRNA. Evidence is presented that the beta-haemoglobin readthrough protein is found in reticulocyte translations and intact cells. Some natural readthrough proteins perform essential functions; they are synthesised through suppression of UGA or UAG but not UAA termination codons.

Allele specific, gene unspecific suppressors in Aspergillus nidulans

Seven suppressor mutations have been isolated in Aspergillus nidulans by coreversion of alleles in physiologically unrelated genes namely, alX, sB, alcA, putative structural genes for allantoinase, sulphate permease and alcohol dehydrogenase respectively. The suppressors are allele specific, gene unspecific. Those described map in four loci, suaA, B, C, D. suaA and suaB are on linkage group III, suaC and suaD on VII. suaB111, suaD103 and suaD108 are semi-dominant in their suppression of alX4 and sB43, suaA101, suaA105 and suaC10. are recessive and have a pleiotropic effect on morphology. SuaC109 is cold sensitive for growth as is sua115, an unmapped mutation on linkage group III which is similar in morphology to suaC109. The two mutations, suaA101 and suaA105 have different spectra of suppression and morphologies. suaA105 weakly suppresses alX4 and sB43 whereas suaA101 strongly suppresses these and alcA125. suaD103 and suaD108 have the same spectrum of suppression. The properties of these suppressors are consistent with their being informational suppressors are consistent with their being informational suppressors of the nonsense type.

Suppression of the nonsense mutation in homozygous beta 0 thalassaemia

The common form of beta thalassaemia associated with elevated haemoglobin A2 levels can be broadly classified as beta + or beta 0 type according to the presence or absence of beta-globin chain synthesis in the homozygous state. The molecular pathology of each type is heterogeneous. Apart from a subgroup of Indo-Pakistani patients, the beta-globin structural gene is intact in the majority of patients with beta 0 thalassaemia. The amount of beta-globin mRNA present in the reticulocytes of these patients varies: in some it is absent or barely detectable; in others, a substantial amount is present, but it is nonfunctional. We recently demonstrated that the molecular lesion in a Chinese patient with nonfunctional beta-globin mRNA was due to the mutation of the normal lysine codon AAG at amino acid 17 to the amber terminator codon UAG, which prematurely terminates the beta-globin chain. In the present study we demonstrate the first example of a nonsense mutation in humans which can be suppressed in vitro by the suppressor tRNA, as has been found in other eukaryotic cells and viruses.

Binding of mammalian ribosomes to MS2 phage RNA reveals an overlapping gene encoding a lysis function

The main binding site for mammalian ribosomes on the single-stranded RNA of bacteriophage MS2 is located nine tenths of the way through the coat protein gene. Translation initiated at an AUG triplet in the +1 frame yields a 75 amino acid polypeptide which terminates within the synthetase gene at a UAA codon, also in the +1 frame. Partial amino acid sequence analysis of the product synthesized in relatively large amounts by mammalian ribosomes confirms this assignment of the overlapping cistron. The same protein is made in an E. coli cell-free system, but only in very small amounts. Analysis of the translation products directed by RNA from op3, a UGA nonsense mutant of phage f2, identifies the overlapping cistron as a lysis gene. In this paper we show that the op3 mutation is a C yield U transition occurring in the second codon of the synthetase cistron, which explains the lowered production of phage replicase (as well as lack of lysis) upon op3 infection of nonpermissive cells. We discuss the properties of the overlapping gene in relation to its lysis function, recognition of the lysis initiator region by E. coli versus eucaryotic ribosomes and op3 as a ribosome binding site mutant for the f2 synthetase cistron.

Identification and nucleotide sequence of the sup8-e UGA-suppressor leucine tRNA from Schizosaccharomyces pombe

Using the translation of rabbit globin mRNA in wheat germ extracts as an assay for ochre and opal suppression, a UGA suppressor tRNA from Schizosaccharomyces pombre strain sup8-e was purified by column chromatography and two-dimensional gel electrophoresis. The purified tRNA can be aminoacylated with leucine by a crude aminoacyl-tRNA synthetase preparation from a wild type S. pombe strain, and has high activity in the suppressor assay. By a combination of post-labeling fingerprinting and rapid gel sequencing methods the nucleotide sequence of this suppressor tRNA was determined to be: pG-C-G-G-C-U-A-U-G-C-C-ac4C-G-A-G-D-G-G-D-G-D-A-A-G-G-G-m22G-G-C-A-G-A-psi-U-U*-C-A-m1G-C-C-C-U-G-C-U-G-U-U-G-U-A-A-A-A-C-G-m5C-G-A-G-A-G-T-psi-C-G-m1A-A-C-C-U-C-U-C-U-G-G-C-C-G-C-A-C-C-AOH. The anticodon sequence U*CA is complementary to the UGA codon. An interesting feature of the suppressor tRNA is an expanded anticodon loop of nine nucleotides owing to an A-C nonpair at the first anticodon stem position.

Characterization of an amber suppressor in Pneumococcus

Partial revertant has been isolated, with resistance to aminopterin intermediate between wild type and mutant. This phenotype is the result of a mutation at a gene unlinked to the amiA locus. This suppressor mutation (su+) has no phenotypic characteristics by itself except a slow growth. 9 amiA mutants (belonging to 6 sites) are affected by su+ out of the 30 investigated mutants (i.e. 22 sites). The efficiency of suppression is site dependent. Two sites out of 14 mutants belonging to the thymidylate synthetase gene are suppressible. Thymidylate synthetase activity is partially restored by su+. Optochin mutants can also be suppressed. Thus su+ is not gene specific but site specific. Moreover when the str-41 allele conferring resistance to streptomycin is introduced by transformation, the suppression effect is restricted. All these properties are characteristic of an informational suppressor. The t-RNA extracted from the suppressor strain su+ but not the wild type restored the synthesis of coat protein coded by RNA from an amber mutant of bacteriophage f2. Attempts to detect ochre suppression activity gave negative results. It is suggested that the su+ gene is amber specific. Thus su+ can provide insight into the nature of suppressible mutations which should be point mutations. Both low efficiency and high efficiency mutants are affected by su+; this is additional evidence that both categories contain point mutations.

Complete nucleotide sequence of the simian-virus 40 Hind-G fragment and localisation of the carboxyl terminus of the VP1 protein

The restriction fragment Hind-G represents 7.0% of the simian virus 40 (SV40) genome. The information present in fragment Hind-G is expressed as part of the major, late 16-S messenger RNA. The complete nucleotide sequence of the fragment Hind-G has now been determined by application of the procedure of Maxam and Gilbert [Proc. Natl Acad. Sci. U.S.A. (1977) 74, 560-564]. It contains 369 nucleotide base pairs. On the basis of the termination code words in the strand with the same polarity as the late mRNA, two illegitimate reading frames can be defined. Therefore the third, open frame must code for the carboxyl terminal part of the VP1 protein. It terminates within fragment Hind-G with a TGA signal. This stop codon is followed by a non-translated region of the mRNA of about 83 nucleotides. The latter contains the sequence A-A-U-A-A-A, common to all other eukaryotic mRNA molecules so far studied. The Hind-G fragment also contains sequences which presumably play a role in the synthesis, processing and/or expression of early mRNA; these aspects are discussed in the following paper.