A novel programed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: Frameshifting without tRNA slippage

Farabaugh, Philip J.; Zhao, Hong; Vimaladithan, Arunachalam

doi:10.1016/0092-8674(93)90297-4

Cited by 155 publications

(143 citation statements)

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“…In contrast, other trinucleotides, e.g. AGT (Farabaugh et al, 1993), CTT (Weiss et al, 1987) and TGA (Craigen and Caskey, 1986;Curran, 1993), may provoke + 1 frameshift. As these trinucleotides belong to X 2 and as X 2 is deduced by two circular permutations of X 0 , the theoretical frame 0 is retrieved with + 1 frameshift, as expected with the examples given.…”

Section: Biological Consequences Which Could Be Associated With the Pmentioning

confidence: 99%

“…Surprisingly, such a property is observed with a biological process, called translational frameshifting, which is involved in: (i) producing a translational fusion for the morphogenesis of the viral particle, e.g. the retroviral gag and pol genes (Farabaugh et al, 1993); e.g. the retrotransposon TYA and TYB genes (Belcourt and Farabaugh, 1990); (ii) regulating gene expression, e.g.…”

Section: Biological Consequences Which Could Be Associated With the Pmentioning

confidence: 99%

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A code in the protein coding genes

Arquès

Michel

1997

Biosystems

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A statistical analysis with 12 288 autocorrelation functions applied in protein (coding) genes of prokaryotes and eukaryotes identifies three subsets of trinucleotides in their three frames: T 0 = X 0 @ {AAA, TTT} with X 0 = {AAC, AAT, ACC, ATC, ATT, CAG, CTC, CTG, GAA, GAC, GAG, GAT, GCC, GGC, GGT, GTA, GTC, GTT, TAC, TTC} in frame 0 (the reading frame established by the ATG start trinucleotide), T 1 = X 1 @ {CCC} in frame 1 and T 2 = X 2 @{GGG} in frame 2 (the frames 1 and 2 being the frame 0 shifted by one and two nucleotides, respectively, to the right). These three subsets are identical in these two gene populations and have five important properties: (i) the property of maximal (20 trinucleotides) circular code for X 0 (resp. X 1 , X 2 ) allowing to retrieve automatically the frame 0 (resp. 1, 2) in any region of the gene without start codon; (ii) the DNA complementarity property C (e.g. C(AAC)= GTT): C(T 0 )=T 0 , C(T 1 )=T 2 and C(T 2 )=T 1 allowing the two paired reading frames of a DNA double helix simultaneously to code for amino acids; (iii) the circular permutation property P (e.g. P(AAC)= ACA): P(X 0 )=X 1 and P(X 1 )=X 2 implying that the two subsets X 1 and X 2 can be deduced from X 0 ; (iv) the rarity property with an occurrence probability of X 0 =6×10 − 8 ; and (v) the concatenation properties in favour of an evolutionary code: a high frequency (27.5%) of misplaced trinucleotides in the shifted frames, a maximum (13 nucleotides) length of the minimal window to retrieve automatically the frame and an occurrence of the four types of nucleotides in the three trinucleotide sites. In Discussion, a simulation based on an independent mixing of the trinucleotides of T 0 allows to retrieve the two subsets T 1 and T 2 . Then, the identified subsets T 0 , T 1 and T 2 replaced in the 2-letter genetic alphabet {R, Y} (R =purine= A or G, Y=pyrimidine= C or T) allow to retrieve the RNY model (N=R or Y) and to explain previous works in the alphabet {R, Y}. Then, these three subsets are related to the genetic code. The trinucleotides of T 0 code for 13 amino acids: Ala, Asn, Asp, Gln, Glu, Gly, Ile, Leu, Lys, Phe, Thr, Tyr and Val. Finally, a strong correlation between the usage of the trinucleotides of T 0 in protein genes and the amino acid frequencies in proteins is observed as six among seven amino acids not coded by T 0 , have as expected the lowest frequencies in proteins of both prokaryotes and eukaryotes.

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Section: Biological Consequences Which Could Be Associated With the Pmentioning

confidence: 99%

Section: Biological Consequences Which Could Be Associated With the Pmentioning

confidence: 99%

A code in the protein coding genes

Arquès

Michel

1997

Biosystems

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“…For both Ty1 and Ty3 retrotransposons, a +1 ribosomal frameshifting event establishes the levels of Gag vs. Gag-Pol fusion proteins. While the precise mechanism of ribosomal frameshifting differs for Ty1 and Ty3, in both cases frameshifting is triggered by a codon that is decoded by a rare tRNA (Belcourt and Farabaugh 1990;Farabaugh et al 1993). The L-A double-stranded RNA virus of yeast likewise encodes both Gag and Pol proteins with the catalytic Pol synthesized as a Gag-Pol fusion by 21 ribosomal frameshifting (Dinman et al 1991).…”

Section: Ribosomal Frameshiftingmentioning

confidence: 99%

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

2016

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In this review, we provide an overview of protein synthesis in the yeast Saccharomyces cerevisiae. The mechanism of protein synthesis is well conserved between yeast and other eukaryotes, and molecular genetic studies in budding yeast have provided critical insights into the fundamental process of translation as well as its regulation. The review focuses on the initiation and elongation phases of protein synthesis with descriptions of the roles of translation initiation and elongation factors that assist the ribosome in binding the messenger RNA (mRNA), selecting the start codon, and synthesizing the polypeptide. We also examine mechanisms of translational control highlighting the mRNA cap-binding proteins and the regulation of GCN4 and CPA1 mRNAs.

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“…Since individual nucleotides flanking rare codons have been linked to frameshifting in a number of systems (Belcourt & Farabaugh, 1990 ;Brierley et al, 1992 ;Farabaugh et al, 1993 ;Jacks et al, 1988 ;Lindsley & Gallant, 1993 ;Shpaer, 1986), the nature of the nucleotides immediately preceding and following the TTA codons was also examined. While no apparent pattern was obvious for the nucleotide 5h of the TTA codon, the nucleotide 3h of the TTA codon appears to be nonrandom with respect to C versus G and T versus A distribution.…”

Section: Discussionmentioning

confidence: 99%

The positive activator of cephamycin C and clavulanic acid production in Streptomyces clavuligerus is mistranslated in a bldA mutant The GenBank accession number for the sequence reported in this paper is AF436078.

et al. 2002

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In Streptomyces coelicolor bldA encodes the principal leucyl tRNA for translation of UUA codons and controls pigmented antibiotic production by the presence of TTA codons in the genes encoding the pathway-specific activators of actinorhodin and undecylprodigiosin biosynthesis. In Streptomyces clavuligerus the gene encoding the pathway-specific activator of both cephamycin C and clavulanic acid production, ccaR, also contains a TTA codon and was expected to exhibit bldA-dependence. A cloned S. clavuligerus DNA fragment containing a sequence showing 91 % identity to the S. coelicolor bldA-encoded tRNA was able to restore antibiotic production and sporulation to bldA mutants of S. coelicolor and the closely related Streptomyces lividans. A null mutation of the bldA gene in S. clavuligerus resulted in the expected sporulation defective phenotype, but unexpectedly had no effect on antibiotic production. Transcript analysis showed no difference in the levels of ccaR transcripts in the wild-type and bldA mutant strains, ruling out any effect of elevated levels of the ccaR mRNA. Furthermore, when compared to the wildtype strain, the bldA mutant showed no differences in the levels of CcaR, suggesting that the single TTA codon in ccaR is mistranslated efficiently. The role of codon context in bldA dependence is discussed.

show abstract

A novel programed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: Frameshifting without tRNA slippage

Cited by 155 publications

References 40 publications

A code in the protein coding genes

A code in the protein coding genes

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

The positive activator of cephamycin C and clavulanic acid production in Streptomyces clavuligerus is mistranslated in a bldA mutant The GenBank accession number for the sequence reported in this paper is AF436078.

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