Coevolution theory of the genetic code at age thirty

Wong, J. Tze‐Fei

doi:10.1002/bies.20208

Cited by 200 publications

(192 citation statements)

References 102 publications

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“…Innovations in the genetic code might also move through populations by horizontal gene transfer (32). It has been suggested that, during early cellular evolution, new genetically encoded amino acids joined more ancient ones as novel biosynthetic pathways arose that used older amino acids and their precursors (33)(34)(35)(36). Newer amino acids joined the growing genetic code by charging of their own tRNA species that allowed interpretation of a codon as the new recruit to the genetic code, even while the older codon function was maintained.…”

Section: Discussionmentioning

confidence: 99%

A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine

Longstaff

Larue

Faust

et al. 2007

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

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Pyrrolysine has entered natural genetic codes by the translation of UAG, a canonical stop codon. UAG translation as pyrrolysine requires the pylT gene product, an amber-decoding tRNA Pyl that is aminoacylated with pyrrolysine by the pyrrolysyl-tRNA synthetase produced from the pylS gene. The pylTS genes form a gene cluster with pylBCD, whose functions have not been investigated. The pylTSBCD gene order is maintained not only in methanogenic Archaea but also in a distantly related Gram-positive Bacterium, indicating past horizontal gene transfer of all five genes. Here we show that lateral transfer of pylTSBCD introduces biosynthesis and genetic encoding of pyrrolysine into a naïve organism. PylS-based assays demonstrated that pyrrolysine was biosynthesized in Escherichia coli expressing pylBCD from Methanosarcina acetivorans. Production of pyrrolysine did not require tRNA Pyl or PylS. However, when pylTSBCD were coexpressed with mtmB1, encoding the methanogen monomethylamine methyltransferase, UAG was translated as pyrrolysine to produce recombinant monomethylamine methyltransferase. Expression of pylTSBCD also suppressed an amber codon introduced into the E. coli uidA gene. Strains lacking one of the pylBCD genes did not produce pyrrolysine or translate UAG as pyrrolysine. These results indicated that pylBCD gene products biosynthesize pyrrolysine using metabolites common to Bacteria and Archaea and, furthermore, that the pyl gene cluster represents a ''genetic code expansion cassette,'' previously unprecedented in natural organisms, whose transfer allows an existing codon to be translated as a novel endogenously synthesized free amino acid. Analogous cassettes may have served similar functions for other amino acids during the evolutionary expansion of the canonical genetic code.T ranslated in-frame amber (TAG/UAG) codons in the genes encoding methylamine methyltransferases from Methanosarcina barkeri (1-3) were early clues to the existence of pyrrolysine as the 22nd genetically encoded amino acid from nature. Crystallography of MtmB1, the monomethylamine methyltransferase, demonstrated that the UAG codon of the encoding mtmB1 gene corresponds to pyrrolysine, whose structure was proposed as lysine with N in amide linkage with the D-isomer of 4-methyl-pyrroline-5-carboxylate (4, 5). This structure is consistent with the UAG-encoded residue's mass in three distinct methylamine methyltransferases (6).Near the mtmB1 gene in Methanosarcina spp. are the pyl genes (ref. 7; Fig. 1). Two of these genes are known to underlie the genetic encoding of pyrrolysine. The pylT encodes tRNA Pyl , whose CUA anticodon complements the UAG codon corresponding to pyrrolysine. Deletion of the pyl gene promoter and pylT leads to loss of pyrrolysine-dependent monomethylamine methyltransferase and methylamine metabolism (8). The pylS gene encodes the pyrrolysyl-tRNA synthetase, PylS, which charges tRNA Pyl with chemically synthesized pyrrolysine and further carries out a pyrrolysine-dependent ATP:pyrophosphate exchange reaction (5, 9-11)...

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Section: Discussionmentioning

confidence: 99%

A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine

Longstaff

Larue

Faust

et al. 2007

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

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“…Relationships between biosynthetic pathways and codon assignments find statistical support in the organization of the present code where biosynthetically related amino acids share codon boxes (Wong 2005). …”

Section: Introductionmentioning

confidence: 79%

Are Proposed Early Genetic Codes Capable of Encoding Viable Proteins?

2014

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Proteins are elaborate biopolymers balancing between contradicting intrinsic propensities to fold, aggregate or remain disordered. Assessing their primary structural preferences observable without evolutionary optimization has been reinforced by the recent identification of de novo proteins that have emerged from previously non-coding sequences. In this paper we investigate structural preferences of hypothetical proteins translated from random DNA segments using the standard genetic code and three of its proposed evolutionarily predecessor models encoding 10, 6 and 4 amino acids, respectively. Our only main assumption is that the disorder, aggregation and transmembrane helix predictions used are able to reflect the differences in the trends of the protein sets investigated. We found that the 10-residue code encodes proteins that resemble modern proteins in their predicted structural properties. All of the investigated early genetic codes give rise to proteins with enhanced disorder and diminished aggregation propensities. Our results suggest that an ancestral genetic code similar to the proposed 10-residue one is capable of encoding functionally diverse proteins but these might have existed under conditions different from today's common physiological ones. The existence of a protein functional repertoire for the investigated earlier stages which is quite distinct as it is today can be deduced from the presented results.

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“…Prebiotic chemistry on early Earth did not supply all 20 current protein amino acids (see part 5.2) and most likely some of them had a biosynthetic origin. The expanding amino acid repertoire might have therefore coevolved with the code, namely new metabolic products could usurp codons previously used by their metabolic precursors (for a recent review, see Wong, 2005). 5.6.1.7.…”

Section: An Expanding Codementioning

confidence: 99%

5. Prebiotic Chemistry – Biochemistry – Emergence of Life (4.4–2 Ga)

et al. 2006

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Abstract. This chapter is devoted to a discussion about the difficulties and even the impossibility to date the events that occurred during the transition from non-living matter to the first living cells. Nevertheless, the attempts to devise plausible scenarios accounting for the emergence of the main molecular devices and processes found in biology are presented including the role of nucleotides at early stages (RNA world). On the other hand, hypotheses on the development of early metabolisms, comEarth, Moon, and Planets (2006) 98: 153-203 Ó Springer 2006

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Coevolution theory of the genetic code at age thirty

Cited by 200 publications

References 102 publications

A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine

A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine

Are Proposed Early Genetic Codes Capable of Encoding Viable Proteins?

5. Prebiotic Chemistry – Biochemistry – Emergence of Life (4.4–2 Ga)

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