The dependence of cell-free protein synthesis in
            <i>E. coli</i>
            upon naturally occurring or synthetic polyribonucleotides

Nirenberg, Marshall W.; Matthaei, Johannes

doi:10.1073/pnas.47.10.1588

Cited by 1,471 publications

(517 citation statements)

References 22 publications

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“…Since the discovery of the standard genetic code (SGC, Nirenberg and Matthaei (1961)), there has been an ongoing discussion on the evolution of this code especially because of its near universality (Vetsigian et al, 2006). This strong conservation inspired many theories on adaptive, historical and chemical arguments assuming that the SGC is optimized for something: It might reflect either the expansion of a more primitive code towards the inclusion of more amino acids, or could be a consequence of direct chemical interactions between RNA and amino acids.…”

Section: Introductionmentioning

confidence: 99%

On the efficiency of the Genetic Code after frameshift mutations

Geyer

Mamlouk

2017

Preprint

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Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes. This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids: We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code -just as for the point mutations -appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other. For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features -just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just "one in a million".

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Section: Introductionmentioning

confidence: 99%

On the efficiency of the Genetic Code after frameshift mutations

Geyer

Mamlouk

2017

Preprint

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“…The two discoveries that the codon TTT, an 'excluded' codon in the concept of code without commas, codes for phenylalanine (Nirenberg and Matthaei, 1961) and that the protein genes are placed in the reading frame with a particular codon, namely the start codon ATG, have led to give up the concept of code without commas in the alphabet {A, C, G, T}. For several biological reasons, in particular the interaction between mRNA and tRNA, the concept of code without commas is resumed later in the alphabet {R, Y} (R= purine= A or G, Y=pyrimidine= C or T) with two codon models for the primitive protein genes: RRY (Crick et al, 1976) and RNY (N= R or Y) (Eigen and Schuster, 1978).…”

Section: Introductionmentioning

confidence: 99%

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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“…The discovery of the genetic code took place between 1961 and 1966 (Nirenberg and Matthaei 1961;Speyer et al 1963;Nirenberg et al 1966;Khorana et al 1966), and immediately inspired the idea of a deep parallel between the genetic code and the codes of language. This idea was expressed in no uncertain terms by George and Muriel Beadle in 1966: "the deciphering of the genetic code has revealed our possession of a language much older than hieroglyphics, a language as old as life itself, a language that is the most living language of all -even if its letters are invisible and its words are buried in the cells of our bodies" (Beadle and Beadle 1966).…”

Section: A Molecular Languagementioning

confidence: 99%

A Short History of Biosemiotics

Barbieri

2009

Biosemiotics

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Biosemiotics is the synthesis of biology and semiotics, and its main purpose is to show that semiosis is a fundamental component of life, i.e., that signs and meaning exist in all living systems. This idea started circulating in the 1960s and was proposed independently from enquires taking place at both ends of the Scala Naturae. At the molecular end it was expressed by Howard Pattee's analysis of the genetic code, whereas at the human end it took the form of Thomas Sebeok's investigation into the biological roots of culture. Other proposals appeared in the years that followed and gave origin to different theoretical frameworks, or different schools, of biosemiotics. They are: (1) the physical biosemiotics of Howard Pattee and its extension in Darwinian biosemiotics by Howard Pattee and by Terrence Deacon, (2) the zoosemiotics proposed by Thomas Sebeok and its extension in sign biosemiotics developed by Thomas Sebeok and by Jesper Hoffmeyer, (3) the code biosemiotics of Marcello Barbieri and (4) the hermeneutic biosemiotics of Anton Markoš. The differences that exist between the schools are a consequence of their different models of semiosis, but that is only the tip of the iceberg. In reality they go much deeper and concern the very nature of the new discipline. Is biosemiotics only a new way of looking at the known facts of biology or does it predict new facts? Does biosemiotics consist of testable hypotheses? Does it add anything to the history of life and to our understanding of evolution? These are the major issues of the young discipline, and the purpose of the present paper is to illustrate them by describing the origin and the historical development of its main schools.

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The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides

Cited by 1,471 publications

References 22 publications

On the efficiency of the Genetic Code after frameshift mutations

On the efficiency of the Genetic Code after frameshift mutations

A code in the protein coding genes

A Short History of Biosemiotics

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