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At least 469 records · Page 26Linked to original sources
PubMed1988

A mutation in the DNA adenine methylase gene (dam) of Salmonella typhimurium decreases susceptibility to 9-aminoacridine-induced frameshift mutagenesis.

A mutant of Salmonella typhimurium with a reduced response to mutation induction by 9-aminoacridine (9AA) has been isolated. The mutation (dam-2) is located in the DNA adenine methylase gene. The dam-2 mutant strain exhibits a level of sensitivity to 2-aminopurine (2AP) intermediate between that of the dam+ and the DNA adenine methylation-deficit dam-1 strain, and 2AP sensitivity was reversed by introduction of a mutH mutation or of the plasmid pMQ148 (which carries a functional Escherichia coli dam+ gene). However, the dam-2 strain is not grossly defective in DNA adenine methylase activity. Whole cell DNA appears full methylated at -GATC- sites. The levels of 9AA required to induce equivalent levels of frameshift mutagenesis in the dam-2 strain were approximately 2-fold higher than for the dam+ strain. Introduction of pMQ148 dam+ reduced the level of 9AA required for induction of frameshift mutations 4-fold in the dam-2 strain and 2-fold in the dam+ strain. The dam-2 mutation had no effect on the levels of ICR191 required for induction of frameshift mutations, but introduction of pMQ148 reduced the ICR191-induced mutagenesis 2-fold. The dam+/pMQ148, dam-2/pMQ148 and dam-1/pMQ148 strains showed identical dose-response curves for both 9AA and ICR191. These results are consistent with a slightly reduced (dam-2) or increased (pMQ148) rate of methylation at the replication fork. The 2AP sensitivity of the dam-2 strain cannot be simply explained. Furthermore, addition of methionine to the assay medium reverses the 2AP sensitivity of the dam-2 strain, but has no effect on 9AA mutagenesis.

Aminacrine↗
PubMed1989

Induced frameshifting mechanism of replication for an information-carrying scrapie prion.

A specific mistranslation mechanism for the replication of an infectious protein is described. The feedback mechanism requires the infectious agent to induce concerted frameshifts during the translation of a cellular gene. Each module of the tandem repeat region of the gene encoding the prion protein (PrP) associated with scrapie infectivity contains multiple sites of potential ribosomal frameshifting. It is proposed that some aberrant variants of PrP containing frameshifted peptides within the octapeptide repeat region of the protein backbone are able to replicate and cause scrapie by interfering with the translation and simultaneous translocation of nascent PrP molecules into the lumen of the endoplasmic reticulum. The model provides a plausible explanation for the behaviour of host-adapted scrapie strains as well as the aetiology of scrapie-like diseases. The hypothesis that a mistranslated PrP is the scrapie agent can also explain discrepancies between the published amino acid sequence of PrP and the sequence deduced from the gene.

Amino Acid Sequence↗
PubMed1991

RNA pseudoknots downstream of the frameshift sites of retroviruses.

RNA pseudoknot structural motifs could have implications for a wide range of biological processes of RNAs. In this study, the potential RNA pseudoknots just downstream from the known and suspected retroviral frame-shift sites were predicted in the Rous sarcoma virus, primate immunodeficiency viruses (HIV-1, HIV-2, and SIV), equine infectious anemia virus, visna virus, bovine leukemia virus, human T-cell leukemia virus (types I and II), mouse mammary tumor virus, Mason-Pfizer monkey virus, and simian SRV-1 type-D retrovirus. Also, the putative RNA pseudoknots were detected in the gag-pol overlaps of two retrotransposons of Drosophila, 17.6 and gypsy, and the mouse intracisternal A particle. For each sequence, the thermodynamic stability and statistical significance of the secondary structure involved in the predicted tertiary structure were assessed and compared. Our results show that the stem-loop structures in the pseudoknots are both thermodynamically highly stable and statistically significant relative to other such configurations that potentially occur in the gag-pol or gag-pro and pro-pol junction domains of these viruses (300 nucleotides upstream and downstream from the possible frameshift sites are included). Moreover, the structural features of the predicted pseudoknots following the frameshift site of pro-pol overlaps of the HTLV-1 and HTLV-2 retroviruses are structurally well conserved. The occurrence of eight compensatory base changes in the tertiary interaction of the two related sequences allow the conservation of their tertiary structures in spite of the sequence divergence. The results support the possible control mechanism for frameshifting proposed by Brierley et al. and Jacks et al.

Base Sequence↗
PubMed1988

Characterization of ribosomal frameshifting in HIV-1 gag-pol expression.

Based on precedents from other retroviruses, the precursor of the human immunodeficiency virus (HIV-1) reverse transcriptase is predicted to be a polyprotein with a relative molecular mass (Mr) of 160,000 (160K) encoded by both the viral pol gene and the upstream gag gene. These two genes lie in different translational reading frames, with the 3' end of gag overlapping the 5' end of pol by 205 or 241 nucleotides. Thus, production of the gag-pol fusion protein would require either messenger RNA processing or translational frameshifting. The latter mechanism has been shown in the synthesis of the gag-pol proteins of two other retroviruses, Rous sarcoma virus (RSV) and mouse mammary tumour virus (MMTV). Here we report that translation of HIV-1 RNA synthesized in vitro by SP6 RNA polymerase yields significant amounts of a gag-pol fusion protein, indicating that efficient ribosomal frameshifting also occurs within the HIV-1 gag-pol overlap region. Site-directed mutagenesis and amino-acid sequencing localized the site of frameshifting to a UUA leucine codon near the 5' end of the overlap.

Amino Acid Sequence↗
PubMed1972

Carcinogens as frameshift mutagens: metabolites and derivatives of 2-acetylaminofluorene and other aromatic amine carcinogens.

Several carcinogenic metabolites of the carcinogen 2-acetyl-aminofluorene, especially 2-nitrosofluorene and N-hydroxy-2-aminofluorene, are potent frameshift mutagens for Salmonella typhimurium. 2-Nitrosonaphthalene, 2-nitrosophenanthrene, 4-nitroso-trans-stilbene, 4-nitrosobiphenyl, and 4-nitrosoazobenzene, all of which are metabolites or likely metabolites of carcinogenic aromatic amines, are also potent frameshift mutagens. These compounds may be frameshift mutagens of the class that intercalates into DNA and then reacts covalently with the DNA; various ultimate carcinogens may be of this type. The utility of a set of bacterial strains for detecting carcinogens as mutagens is shown.

Acetamides↗
PubMed1974

Chemical carcinogens as frameshift mutagens: Salmonella DNA sequence sensitive to mutagenesis by polycyclic carcinogens.

Other investigators have shown that several polycyclic carcinogens are frameshift mutagens in Salmonella. Mutagenic potency of these compounds is assessed by ability to induce reversion of histidine-requiring frameshift mutants to prototrophy. One frameshift mutation in the histidinol dehydrogenase gene, hisD3052, is unusually sensitive to mutagenesis by certain polycyclic carcinogens. We find that the 3052 mutation is a - 1 deletion, probably loss of a G.C pair from a DNA repeat of [unk]. The polycyclic carcinogens tested (e.g., 2-nitroso-fluorene) revert 3052 by deleting a [unk] doublet from the DNA sequence [unk], which is close to the 3052 site. This rare mispairing-prone sequence represents the carcinogen-sensitive "hotspot" in 3052. The ICR compounds, noncarcinogenic intercalating agents, show a broader specificity of mutagenesis. Reversion with these mutagens occurs predominantly by two mechanisms: one identical to that of the polycyclic carcinogens, and the other by +1 additions in a third DNA tract narrowly separated from the 3052 site. The alkylating carcinogen N-methyl-N'-nitro-N-nitrosoguanidine appears to have a similar dual specificity. DNA base changes in 3052 revertants have been correlated with properties of histidinol dehydrogenase in crude extracts. This correlation of DNA base sequence with electrophoretic and other properties of the mutant proteins allows one to analyze easily the specificity of new mutagens that mutate this strain.

Acridines↗
PubMed1986

tRNA anticodon replacement experiments show that ribosomal frameshifting can be caused by doublet decoding.

The expression of certain normal genes requires a specific ribosomal frameshift event because the mRNA has the coding information for one protein in two different reading frames. One of several possible mechanisms for this involves recognition of a nontriplet codon by a noncognate tRNA. The AGUC-decoding Escherichia coli tRNASer3 reads a GCA alanine codon to cause a -1 frameshift. Replacement of the anticodon of tRNAPhe with the anticodon of tRNASer3 allows the constructed tRNA to cause this frameshifting. By altering the anticodon loop nucleotides at positions 33-36 in the constructed tRNAPhe molecules, the tRNA was found to recognize a 2-base codon. Instead of the usual anticodon, positions 34-36, the nucleotides in positions 34 and 35 form essential base pairs with the first two positions of the alanine codon. The uridine in position 36 is also required but not for base pairing.

Anticodon↗
PubMed1988

Efficient translational frameshifting occurs within a conserved sequence of the overlap between the two genes of a yeast Ty1 transposon.

The Ty (transposon yeast) family of retroviral-like transposons include two genes, TYA and TYB, analogous to the gag and pol genes of metazoan retroviruses. TYB lies downstream of TYA, the two genes overlapping by 38 base pairs. The primary translation product of TYB is a TYA/TYB fusion protein whose expression has been inferred to occur by translational frameshifting within the overlap region. We show that the event leading to expression of TYB is very efficient, resulting in 20% read-through into TYB from TYA. We demonstrate that the Ty mRNA is colinear with the DNA sequence of the element, eliminating any pretranslational model for TYB expression. Frameshifting requires no particular sequence of the upstream TYA gene, nor any global RNA structure. Surprisingly, it can be promoted by a 14-base-pair oligonucleotide of the overlap region. The ability of this oligonucleotide to function is inhibited when it is positioned immediately downstream of an initiator AUG. We conclude that the TYB gene is expressed by an efficient ribosomal frameshifting event requiring a small oligonucleotide sequence derived from the TYA/TYB overlap region.

Amino Acid Sequence↗
PubMed1989

Frameshifting is required for production of the transposase encoded by insertion sequence 1.

Insertion sequence IS1 has two coding frames, insA and insB, which are essential for its transposition. Here, we show that a frameshifting event in the -1 direction from the 3' end region of the insA frame to an open reading frame (B' frame), extending from the 5' end of the insB frame, is involved in production of the InsA-B'-InsB fusion protein that has IS1 transposase activity. The frameshifting event is likely to have occurred at the sequence AAAAAC where the insA frame overlaps the B' frame. Interestingly, this sequence is also present in one of the two sequences identified in retroviruses as frameshift signals for production of transframe polyproteins from the overlapping genes gag-pro or gag-pro-pol.

Amino Acid Sequence↗
PubMed1992

Ribosomal movement impeded at a pseudoknot required for frameshifting.

Translational frameshifting sometimes occurs when ribosomes encounter a "shift" site preceding a region of unusual secondary structure, which in at least three cases is known to be a pseudoknot. We provide evidence that ribosomes have a decreased rate of movement through a pseudoknot required for frameshifting. These paused ribosomes are directly situated over the shift sequence. Ribosomal pausing appears to be necessary but not sufficient for frameshifting.

Animals↗
PubMed1994

Spermidine deficiency increases +1 ribosomal frameshifting efficiency and inhibits Ty1 retrotransposition in Saccharomyces cerevisiae.

Polyamines have been implicated in nucleic acid-related functions and in protein biosynthesis. RNA sequences that specifically direct ribosomes to shift reading frame in the -1 and +1 directions may be used to probe the mechanisms controlling translational fidelity. We examined the effects of spermidine on translational fidelity by an in vivo assay in which changes in beta-galactosidase activity are dependent on yeast retrovirus Ty +1 and yeast double-stranded RNA virus L-A -1 ribosomal frameshifting signals. In spe2 delta mutants of Saccharomyces cerevisiae, which cannot make spermidine as a result of a deletion in the SPE2 gene, there is a marked elevation in +1 but no change in -1 ribosomal frameshifting. The increase in +1 ribosomal frameshifting efficiency is accompanied by a striking decrease in Ty1 retrotransposition.

Adenosylmethionine Decarboxylase↗
PubMed1990

Induction of specific frameshift and base substitution events by benzo[a]pyrene diol epoxide in excision-repair-deficient Escherichia coli.

We have determined the DNA alterations recovered after treatment with (+-)-r-7,t-8-dihydroxy-t-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(+-)-anti-BPDE] in the lacI gene of excision-repair-deficient (Uvr-) Escherichia coli. The high induction of -(G:C) frameshifts, G:C----T:A and A:T----T:A transversions, and the presence of complex mutations of a particular motif, distinguish the mutational distribution recovered in the Uvr- strain, although other mutational classes, including -(A:T) frameshifts and duplications, were also moderately induced. The great majority of -(G:C) frameshifts, the predominant mutation recovered, occurred in runs of G residues. The G:C----T:A transversion was found to occur more frequently (10/12 occurrences) at 5'-Y-G-3' sites, sequences at which the labile BPDE:N7G adduct has been predicted to occur. Moreover, the relative proportions of G:C----T:A, A:T----T:A and G:C----A:T mutations correlate well with the expected proportions of alkali-labile lesions at G, A and C residues. These results support the model that (+-)-anti-BPDE-induced base substitution mutagenesis in E.coli proceeds through abasic intermediates across from which adenine is preferentially incorporated during replication.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1982

Frameshift suppression in Saccharomyces cerevisiae. V. Isolation and genetic properties of nongroup-specific suppressors.

Two classes of frameshift suppressors distributed at 22 different loci were identified in previous studies in the yeast Saccharomyces cerevisiae. These suppressors exhibited allele-specific suppression of +1 G:C insertion mutations in either glycine or proline codons, designated as group II and group III frameshift mutations, respectively. Genes corresponding to representative suppressors of each group have been shown to encode altered glycine or proline tRNAs containing four base anticodons.--This communication reports the existence of a third class of frameshift suppressor that exhibits a wider range in specificity of suppression. The suppressors map at three loci, suf12, suf13, and suf14, which are located on chromosomes IV, XV, and XIV, respectively. The phenotypes of these suppressors suggest that suppression may be mediated by genes other than those encoding the primary structure of glycine or proline tRNAs.

Chromosome Mapping↗
PubMed1980

Frameshift suppression Saccharomyces cerevisiae. II. Genetic properties of group II suppressors.

Suppressors of ICR-induced mutations that exhibit behavior similar to bacterial frameshift suppressors have been identified in the yeast Saccharomyces cerevisiae. The yeast suppressors have been divided into two groups. One of these groups (Group II: SUF1, SUF3, SUF4, SUF5 and SUF6) appears to include a set of informational suppressors in which the vehicle of suppression is glycyl-tRNA. Some of the genetic properties of Group II suppressors are described in this communication.--Corevertants of the Group II frameshift mutations his4-519 and leu2-3 have been characterized to determine the spectrum of reversion events induced by the frameshift mutagen ICR-170. Seventy-three ICR-induced corevertants were analyzed. With the exception of one cerevertant, which carried an allele of SUF1, all carried alleles of SUF3 or SUF5. SUF1, SUF3, SUF4 and SUF6 were represented among spontaneous and UV-induced corevertants. In the course of these experiments one of the suppressors was mapped. SUF5, the probable structural gene for tRNAGLY1, is located between ade2 and ade9 on chromosome XV.--SUF1, SUF4 and SUF6 have novel properties and comprise a distinct subset of suppressors. Although these suppressors show no genetic linkage to each other, they share several common features including lethality in haploid pairwise combinations, reduced tRNAGLY3 isoacceptor activity and increased efficiency of suppression in strains carrying the cytoplasmically inherited [PSI] element. In addition, strains carrying SUF1, SUF4 or SUF6 are phenotypically unstable and give rise to mitotic Suf+ segments at high frequency. These segregants invariably contain a linked, second-site mutation that maps in or adjacent to the suppressor gene itself. Strains carrying any of these suppressors also give rise to mitotic segregants that exhibit enhanced efficiency of suppression; mutations responsible for this phenotype map at two loci, upf1 and upf2. These genes show no genetic linkage to any of the group II suppressors.--Methods that permit positive selection have been devised in order to examine large numbers of variants. The importance of these interacting mutants is underscored by their potential utility in studying suppressor function at the molecular level.

Chromosome Mapping↗
PubMed1989

Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses.

RNA stem-loop structures situated just 3' to the frameshift sites of the retroviral gag-pol or gag-pro and pro-pol regions may make important contributions to frame-shifting in retroviruses. In this study, the thermodynamic stability and statistical significance of such secondary structural features relative to others in the sequence have been assessed using a newly developed method that combines calculations of the lowest free energy of formation of RNA secondary structures and the Monte Carlo simulations. Our results show that stem-loop structures situated just 3' to the frameshift sites are both highly stable and statistically significant relative to others in the gag-pol or gag-pro and pro-pol junction domains (both 300 nucleotides upstream and downstream from the possible frameshift sites are included) of Rous sarcoma virus (RSV), human immunodeficiency virus (HIV-1), bovine leukemia virus (BLV), human T-cell leukemia virus type II (HTLV-II), and mouse mammary tumor virus (MMTV). No other more stable, or significant folding regions are predicted in these domains.

Avian Sarcoma Viruses↗
PubMed1990

The primary structure and expression of the second open reading frame of the polymerase gene of the coronavirus MHV-A59; a highly conserved polymerase is expressed by an efficient ribosomal frameshifting mechanism.

Sequence analysis of a substantial part of the polymerase gene of the murine coronavirus MHV-A59 revealed the 3' end of an open reading frame (ORF1a) overlapping with a large ORF (ORF1b; 2733 amino acids) which covers the 3' half of the polymerase gene. The expression of ORF1b occurs by a ribosomal frameshifting mechanism since the ORF1a/ORF1b overlapping nucleotide sequence is capable of inducing ribosomal frameshifting in vitro as well as in vivo. A stem-loop structure and a pseudoknot are predicted in the nucleotide sequence involved in ribosomal frameshifting. Comparison of the predicted amino acid sequence of MHV ORF1b with the amino acid sequence deduced from the corresponding gene of the avian coronavirus IBV demonstrated that in contrast to the other viral genes this ORF is extremely conserved. Detailed analysis of the predicted amino acid sequence revealed sequence elements which are conserved in many DNA and RNA polymerases.

Amino Acid Sequence↗
PubMed1994

Regulatory implications of translational frameshifting in cellular gene expression.

The genetic code, once thought to be rigid, has been found to be quite flexible, permitting several different reading alternatives. One of these is translational frameshifting, a process programmed in the mRNA sequence and which enables a +1 or -1 shift from the reading frame of the initiation codon. So far, the involvement of translational frameshifting in gene expression has been described mainly in viruses (particularly retroviruses), retrotransposons, and bacterial insertion elements. In this MicroReview, we present a survey of the cellular genes, mostly in Escherichia coli, which have been found to be expressed through a translational frameshifting process, as well as a discussion of the regulatory implications of this process.

Base Sequence↗
PubMed1985

The pho1 mutation. A frameshift, and its compensation, producing altered forms of physiologically efficient ATPase in yeast mitochondria.

The pho1 mutation belongs to the OL12 gene on mitochondrial DNA of Saccharomyces cerevisiae, which codes for a membrane factor subunit of the mitochondrial ATPase (apparent molecular mass 20 kDa). We analysed the ATPase complex from the pho1 mutant and from three revertants, after immunoprecipitation from mitochondrial extracts, by dodecyl sulphate/acrylamide gel electrophoresis. In two revertants the OL12 gene product appeared as an abundant slower migrating peptide, while in the pho mutant, two bands appeared in very low amounts. For the third revertant, a strong band appeared at the normal level. Sequencing of the OL12 gene from these strains gave the following results: the pho1 mutation is a frameshift, arising by insertion of an extra thymidine into a group of three. Two of the revertants contain the same group of four thymidines, but genetic compensation of the frameshift occurs 24 base pairs downstream by the loss of four bases, implying a deficit of one codon. The third revertant has recovered the normal three-thymidine sequence. There is excellent correlation between the modified sequences and electrophoretic migration of the peptide product. Owing to the leakiness of the pho1 phenotype (reduced but not nil growth rate on oxidizable carbon sources, 5-10% highly oligomycin-sensitive ATPase complex, low amounts of OL12 gene product peptides), some translational correction of the frameshift is bound to occur. Based on these results, the compatibility of abnormal ATPase architecture with modified energetic efficiency is discussed.

Adenosine Triphosphatases↗