A quantitative investigation of the chemical space surrounding amino acid alphabet formation

Lü, Yi; Freeland, Stephen J.

doi:10.1016/j.jtbi.2007.10.007

Cited by 22 publications

(11 citation statements)

References 100 publications

(112 reference statements)

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“…, (24–27) for hypotheses on the evolution of the code through a “doublet” phase). Questions on why there are four standard nucleotides in the code (28, 29) or why the standard code encodes 20 amino acids (30–32) are fully legitimate. Conceivably, theories on the early phases of the evolution of the code should be constrained by the minimal complexity that is required of a self‐replicating system ( e.g.…”

Section: Introductionmentioning

confidence: 99%

Origin and evolution of the genetic code: The universal enigma

2008

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The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on the origin and evolution of the code are the stereochemical theory, according to which codon assignments are dictated by physico-chemical affinity between amino acids and the cognate codons (anticodons); the coevolution theory, which posits that the code structure coevolved with amino acid biosynthesis pathways; and the error minimization theory under which selection to minimize the adverse effect of point mutations and translation errors was the principal factor of the code’s evolution. These theories are not mutually exclusive and are also compatible with the frozen accident hypothesis, i.e., the notion that the standard code might have no special properties but was fixed simply because all extant life forms share a common ancestor, with subsequent changes to the code, mostly, precluded by the deleterious effect of codon reassignment. Mathematical analysis of the structure and possible evolutionary trajectories of the code shows that it is highly robust to translational misreading but there are numerous more robust codes, so the standard code potentially could evolve from a random code via a short sequence of codon series reassignments. Thus, much of the evolution that led to the standard code could be a combination of frozen accident with selection for error minimization although contributions from coevolution of the code with metabolic pathways and weak affinities between amino acids and nucleotide triplets cannot be ruled out. However, such scenarios for the code evolution are based on formal schemes whose relevance to the actual primordial evolution is uncertain. A real understanding of the code origin and evolution is likely to be attainable only in conjunction with a credible scenario for the evolution of the coding principle itself and the translation system.

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Section: Introductionmentioning

confidence: 99%

Origin and evolution of the genetic code: The universal enigma

2008

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“…Many aspects of this selection have remained unsettled despite intense intellectual efforts, such that the evolution of the genetic code has occasionally been termed the "universal enigma" of biology (1). Specifically, the choice of the proteinogenic AAs out of a much larger prebiotic and metabolic pool has remained hardly understood, even if a core triad of attributes (size, charge, and hydrophobicity) probably played a major role, especially in the beginning (2). At the same time, theoretical and statistical investigations have clearly suggested that the choice of AAs to be encoded by the standard genetic code was nonrandom and adaptive (2)(3)(4).…”

mentioning

confidence: 99%

“…Attractive candidates to trigger the introduction of new AAs into the genetic code are properties that would enable an improved folding of proteins or higher protein stability (2,5). Surprisingly, though, investigations on the minimum number of different AA types required to build a foldable polypeptide have concluded that, in general, this number is only about 7-13 (5)(6)(7)(8)(9) and may be as low as 3 (10).…”

mentioning

confidence: 99%

Modern diversification of the amino acid repertoire driven by oxygen

Granold

Hajieva

Toşa

et al. 2017

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

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All extant life employs the same 20 amino acids for protein biosynthesis. Studies on the number of amino acids necessary to produce a foldable and catalytically active polypeptide have shown that a basis set of 7–13 amino acids is sufficient to build major structural elements of modern proteins. Hence, the reasons for the evolutionary selection of the current 20 amino acids out of a much larger available pool have remained elusive. Here, we have analyzed the quantum chemistry of all proteinogenic and various prebiotic amino acids. We find that the energetic HOMO–LUMO gap, a correlate of chemical reactivity, becomes incrementally closer in modern amino acids, reaching the level of specialized redox cofactors in the late amino acids tryptophan and selenocysteine. We show that the arising prediction of a higher reactivity of the more recently added amino acids is correct as regards various free radicals, particularly oxygen-derived peroxyl radicals. Moreover, we demonstrate an immediate survival benefit conferred by the enhanced redox reactivity of the modern amino acids tyrosine and tryptophan in oxidatively stressed cells. Our data indicate that in demanding building blocks with more versatile redox chemistry, biospheric molecular oxygen triggered the selective fixation of the last amino acids in the genetic code. Thus, functional rather than structural amino acid properties were decisive during the finalization of the universal genetic code.

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“…This is a chemical analytical task. Specifically, it should look for subsets of equivalent molecules, such as alpha versus beta amino acids (Lu & Freeland 2008), mono-halogenated versus multiply halogenated hydrocarbons (Biemann et al 1976(Biemann et al , 1977Bains 2013), or compounds with highly biased chirality (Levin 2009;Sun et al 2009;Warmflash et al 2009). …”

Section: Practical Detection Of Lifementioning

confidence: 99%

What do we think life is? A simple illustration and its consequences

Bains¹

2013

International Journal of Astrobiology

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The conundrum of finding a 'definition' for life can be side-stepped by asking how people actually identify examples of life, and using this as the basis for life detection strategies. I illustrate how astrobiologists actually select things that are living from things that are not living with a simple exercise, and use this as the starting point to develop four characteristics that underlie their decisions: highly distinctive structure (physical or chemical), dynamic behaviour (physical or chemical), multiple instances of life forming a 'natural group' and that the structural and dynamic characteristics of the group are independent of the details of the substrate on which life is growing. I show that these all derive the role of a code in the dynamic maintenance and propagation of life. I argue that evolution is neither a useful nor a practical way of identifying life. I conclude with some specific ways that these general categories of the observable properties of life can be detected.

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A quantitative investigation of the chemical space surrounding amino acid alphabet formation

Cited by 22 publications

References 100 publications

Origin and evolution of the genetic code: The universal enigma

Origin and evolution of the genetic code: The universal enigma

Modern diversification of the amino acid repertoire driven by oxygen

What do we think life is? A simple illustration and its consequences

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