Unassigned Codons, Nonsense Suppression, and Anticodon Modifications in the Evolution of the Genetic Code

Gulik, Peter T. S. van der; Hoff, Wouter D.

doi:10.1007/s00239-011-9470-3

Cited by 20 publications

(18 citation statements)

References 66 publications

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“…Since the UNN anticodon is inherently capable of two-out-of-three reading, some solution has to be developed to disallow misreading of Y-3rd codons by UNN anticodon in a 2aa box [51,52]. In the course of genetic code evolution, primitive organisms about to acquire Stage 2 wobble had to choose between two solutions to this challenge [53,54]:…”

Section: Misreading By the Unn Anticodonmentioning

confidence: 99%

“…Although the presence of unassigned codons that are not assigned to any amino acid or termination signal could be detrimental to an organism, the extent of the detriment might not always be severe [53], and unassigned codons are also known to exist in organisms [60,61]. Moreover, when the CCA codon is entirely retired from the proteome, it becomes an absent codon rather than an unassigned codon and unable to cause damage except where it reappears through random point mutations.…”

Section: Misreading By the Unn Anticodonmentioning

confidence: 99%

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Future of the Genetic Code

Xue

Wong

2017

Life

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The methods for establishing synthetic lifeforms with rewritten genetic codes comprising non-canonical amino acids (NCAA) in addition to canonical amino acids (CAA) include proteome-wide replacement of CAA, insertion through suppression of nonsense codon, and insertion via the pyrrolysine and selenocysteine pathways. Proteome-wide reassignments of nonsense codons and sense codons are also under development. These methods enable the application of NCAAs to enrich both fundamental and applied aspects of protein chemistry and biology. Sense codon reassignment to NCAA could incur problems arising from the usage of anticodons as identity elements on tRNA, and possible misreading of NNY codons by UNN anticodons. Evidence suggests that the problem of anticodons as identity elements can be diminished or resolved through removal from the tRNA of all identity elements besides the anticodon, and the problem of misreading of NNY codons by UNN anticodon can be resolved by the retirement of both the UNN anticodon and its complementary NNA codon from the proteome in the event that a restrictive post-transcriptional modification of the UNN anticodon by host enzymes to prevent the misreading cannot be obtained.

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Section: Misreading By the Unn Anticodonmentioning

confidence: 99%

Section: Misreading By the Unn Anticodonmentioning

confidence: 99%

Future of the Genetic Code

Xue

Wong

2017

Life

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“…Unmodified U in the first anticodon position recognizes all four codons rather efficiently, but only in the eight fourfold degenerate codon boxes [ 33 ]. These six facts together give us the information that at a certain stage in the development of life (well before the last universal common ancestor) a tRNA set containing 8 U-starting anticodons, 8 G-starting anticodons, and 8 C-starting anticodons existed [ 14 , 34 ] which produced remarkably complete (in terms of number of amino acids) and unambiguous genetic coding. It is this kind of biochemical facts which gives us information concerning the origin of life, not space exploration.…”

Section: The Information Frozen In the Genetic Codementioning

confidence: 99%

On the Origin of Sequence

Gulik

2015

Life

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Three aspects which make planet Earth special, and which must be taken in consideration with respect to the emergence of peptides, are the mineralogical composition, the Moon which is in the same size class, and the triple environment consisting of ocean, atmosphere, and continent. GlyGly is a remarkable peptide because it stimulates peptide bond formation in the Salt-Induced Peptide Formation reaction. The role glycine and aspartic acid play in the active site of RNA polymerase is remarkable too. GlyGly might have been the original product of coded peptide synthesis because of its importance in stimulating the production of oligopeptides with a high aspartic acid content, which protected small RNA molecules by binding Mg2+ ions. The feedback loop, which is closed by having RNA molecules producing GlyGly, is proposed as the essential element fundamental to life. Having this system running, longer sequences could evolve, gradually solving the problem of error catastrophe. The basic structure of the standard genetic code (8 fourfold degenerate codon boxes and 8 split codon boxes) is an example of the way information concerning the emergence of life is frozen in the biological constitution of organisms: the structure of the code contains historical information.

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“…However, little attention has been paid to stage 2. In [ 10 ], we drew attention to the fact that a relatively small tRNA set with unmodified anticodons is able to unambiguously read more than 80% of the codons of the genetic code. As discussed below, evidence has accumulated [ 11 – 14 ] that an important fundamental regularity exists in the SGC, which provides key constraints on its evolutionary origin.…”

Section: Introductionmentioning

confidence: 99%

Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code

Gulik

Hoff

2016

PLoS ONE

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Based on (i) an analysis of the regularities in the standard genetic code and (ii) comparative genomics of the anticodon modification machinery in the three branches of life, we derive the tRNA set and its anticodon modifications as it was present in LUCA. Previously we proposed that an early ancestor of LUCA contained a set of 23 tRNAs with unmodified anticodons that was capable of translating all 20 amino acids while reading 55 of the 61 sense codons of the standard genetic code (SGC). Here we use biochemical and genomic evidence to derive that LUCA contained a set of 44 or 45 tRNAs containing 2 or 3 modifications while reading 59 or 60 of the 61 sense codons. Subsequent tRNA modifications occurred independently in the Bacteria and Eucarya, while the Archaea have remained quite close to the tRNA set as it was present in LUCA.

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Unassigned Codons, Nonsense Suppression, and Anticodon Modifications in the Evolution of the Genetic Code

Cited by 20 publications

References 66 publications

Future of the Genetic Code

Future of the Genetic Code

On the Origin of Sequence

Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code

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