The RNA Code and Protein Synthesis

Nirenberg, Marshall W.; Caskey, Thomas; Marshall, Richard; Brimacombe, Richard; Kellogg, Donald A.; Doctor, Bhupendra P.; Hatfield, Dolph L.; Levin, Joseph; Rottman, Fritz M.; Pestka, Sidney; Wilcox, Michael; Anderson, Felicity

doi:10.1101/sqb.1966.031.01.008

Cited by 178 publications

(72 citation statements)

References 36 publications

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“…This degeneracy of the genetic code has puzzled biologists since the code was 34 cracked [Khorana et al, 1966, Nirenberg et al, 1966. One explanation of this 35 phenomenon was suggested by Francis Crick, who assumed that only the first two codon 36 positions were important in a primordial code [Crick, 1968].…”

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confidence: 99%

The structure of the genetic code as an optimal graph clustering problem

Błażej

Wnętrzak

et al. 2018

Preprint

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The standard genetic code (SGC) is the set of rules by which genetic information is 1 translated into proteins, from codons, i.e. triplets of nucleotides, to amino acids. The 2 questions about the origin and the main factor responsible for the present structure of sequences generated by single nucleotide substitutions. We described the genetic code as 10 a partition of an undirected and unweighted graph, which makes the model general and 11 universal. Using this approach, we showed that the structure of the genetic code is a 12 solution to the graph clustering problem. We presented and discussed the structure of 13 the codes that are optimal according to the conductance. Despite the fact that the 14 standard genetic code is far from being optimal according to the conductance, its 15 structure is characterised by many codon groups reaching the minimum conductance for 16 their size. The SGC represents most likely a local minimum in terms of errors occurring 17 in protein-coding sequences and their translation.

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confidence: 99%

The structure of the genetic code as an optimal graph clustering problem

Błażej

Wnętrzak

et al. 2018

Preprint

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“…The (+ -) mRNA segment encodes a segment of altered amino acids in the polypeptide chain, often disturbing its function. Sequencing the affected polypeptide segment allows reconstruction of associated mRNA and DNA sequences (9,10).…”

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confidence: 99%

Chemical Carcinogens as Frameshift Mutagens: Salmonella DNA Sequence Sensitive to Mutagenesis by Polycyclic Carcinogens

Isono

Yourno

1974

Proc. Natl. Acad. Sci. U.S.A.

138

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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 -G-G-G--C-C-C-. The polycyclic carcinogens tested (e.g., 2-nitroso- Frameshift mutations result from additions (+) or deletions (-) of DNA base pairs from genes encoding polypeptide chains, so that triplets in the product mRNA are not read in the correct frame after the mutation (7,8). Correction of such mutations may occur by restoration of the original base sequence, or by introduction of a closely positioned frameshift of opposite sign. In these double frameshift mutants (+ -) the normal reading frame is restored in mRNA except for the segment between the two frameshifts. The (+ -) mRNA segment encodes a segment of altered amino acids in the polypeptide chain, often disturbing its function. Sequencing the affected polypeptide segment allows reconstruction of associated mRNA and DNA sequences (9, 10). The hisD gene encodes the enzyme histidinol dehydrogenase (EC 1.1.1.23). To determine nucleic acid base changes in 3052 caused by polycyclic carcinogens and other frameshift mutagens, we have induced reversion in 3052 by these compounds. Revertants carrying double frameshift mutations were detected by rapid screening of crude extracts from revertants for altered histidinol dehydrogenase. The altered enzyme from each double mutant was then purified and compared with the normal enzyme by peptide mapping to detect altered peptides. These were sequenced to reconstruct altered DNA sequences in 3052 and its revertants. We have also classified the reversions with respect to certain properties of histidinol dehydrogenase from crude extracts, and have correlated the classes of reversion with specific DNA sequence changes.We believe that this newly characterized tester system will be useful for rapid screening of carcinogens as frameshift mutagens. For the relatively small effort of inducing reversions in 3052 with carcinogens or other mutagens and examining crude extract histidinol dehydrogenase, it should be possible to assign the reversions to the standard groups with known base sequence changes in DNA (see below).

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“…Although responses of Gly-tRNA to the glycine codons, GGU, GGC, and GGA, (21) and of Leu-tRNA to the leucine codons, UUG and UUA, (21) were observed, no responses of these aminoacyl-tRNAs were observed to codon UGA (data not shown).…”

Section: Aminoacyl-trna Responses To Codonsmentioning

confidence: 85%

“…['4C]Cys-tRNA in Fractions II and III responded to the cysteine codons UGU and UGC (21) and slightly to codon UGA ( Table 2). Responses of fractionated Cys-tRNA of guinea-pig liver to the cysteine codons and to UGA have been reported by Caskey et al (9).…”

Section: Aminoacyl-trna Responses To Codonsmentioning

confidence: 99%

Recognition of Nonsense Codons in Mammalian Cells

Hatfield

1972

Proc. Natl. Acad. Sci. U.S.A.

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The tritiated trinucleotide UGA was used in a binding assay to detect transfer RNAs that recognize this nonsense codon from calf-liver cells. Acylation of transfer RNA with labeled amino acids and determination of codon responses of aminoacyl-tRNAs demonstrate that a species of seryl-tRNA and a species of arginyltRNA recognize the codon UGA. Slight responses of cysteinyl-tRNA and of trytophanyl-tRNA to the codon UGA were also observed.

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The RNA Code and Protein Synthesis

Cited by 178 publications

References 36 publications

The structure of the genetic code as an optimal graph clustering problem

The structure of the genetic code as an optimal graph clustering problem

Chemical Carcinogens as Frameshift Mutagens: Salmonella DNA Sequence Sensitive to Mutagenesis by Polycyclic Carcinogens

Recognition of Nonsense Codons in Mammalian Cells

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