Initiating translation with <i>D</i>-amino acids

Murakami, Hiroshi; Suga, Hiroaki

doi:10.1261/rna.1020708

Cited by 115 publications

(89 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Several attempts to recode the N-terminus of proteins with ncAAs have been pursued, mostly using in vitro approaches. [64][65][66][67][68] Interestingly, several Met analogues are known to work in protein initiation in vivo, indicating that they are formylated by methionyl-tRNA fMet formyltransferase (FMT) and recognized by the initiation factors (IFs). [69] In addition, their N-terminal processing is attenuated [69] and can be regulated by changing the identity of the second amino acid in the protein sequence.…”

Section: Site-specific Reassignment Of the Aug Codonmentioning

confidence: 99%

Towards Reassignment of the Methionine Codon AUG to Two Different Noncanonical Amino Acids in Bacterial Translation

Simone¹,

Acevedo‐Rocha²,

Hoesl³

et al. 2016

Croat. Chem. Acta

View full text Add to dashboard Cite

Genetic encoding of noncanonical amino acids (ncAAs) through sense codon reassignment is an efficient tool for expanding the chemical functionality of proteins. Incorporation of multiple ncAAs, however, is particularly challenging. This work describes the first attempts to reassign the sense methionine (Met) codon AUG to two different ncAAs in bacterial protein translation. Escherichia coli methionyl-tRNA synthetase (MetRS) charges two tRNAs with Met: tRNA fMet initiates protein synthesis (starting AUG codon), whereas elongator tRNA Met participates in protein elongation (internal AUG codon(s)). Preliminary in vitro experiments show that these tRNAs can be charged with the Met analogues azidohomoalanine (Aha) and ethionine (Eth) by exploiting the different substrate specificities of EcMetRS and the heterologous MetRS / tRNA Met pair from the archaeon Sulfolobus acidocaldarius, respectively. Here, we explored whether this configuration would allow a differential decoding during in vivo protein initiation and elongation. First, we eliminated the elongator tRNA Met from a methionine auxotrophic E. coli strain, which was then equipped with a rescue plasmid harboring the heterologous pair. Although the imported pair was not fully orthogonal, it was possible to incorporate preferentially Eth at internal AUG codons in a model protein, suggesting that in vivo AUG codon reassignment is possible. To achieve full orthogonality during elongation, we imported the known orthogonal pair of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) / tRNA Pyl and devised a genetic selection system based on the suppression of an amber stop codon in an important glycolytic gene, pfkA, which restores enzyme functionality and normal cellular growth. Using an evolved PylRS able to accept Met analogues, it should be possible to reassign the AUG codon to two different ncAAs by using directed evolution.

show abstract

Section: Site-specific Reassignment Of the Aug Codonmentioning

confidence: 99%

Towards Reassignment of the Methionine Codon AUG to Two Different Noncanonical Amino Acids in Bacterial Translation

Simone¹,

Acevedo‐Rocha²,

Hoesl³

et al. 2016

Croat. Chem. Acta

View full text Add to dashboard Cite

show abstract

“…When elongation tRNAs carrying D-amino acids are presented to the ribosome in vitro they are incorporated extremely poorly, but incorporated nevertheless (Yamane et al 1981;Heckler et al 1988). It has recently been found that peptide synthesis can be effectively initiated with D-amino acids (Goto et al 2008). In addition, by introducing mutations in the PTC region and/or other nearby regions of the 23S rRNA, it was possible to obtain enhanced tolerance of D-amino acids in vitro (Starck et al 2003;Tan et al 2004;Dedkova et al 2003 and2006).…”

Section: Chirality and The Ribosomementioning

confidence: 99%

Origin and Evolution of the Ribosome

Fox¹

2010

Cold Spring Harbor Perspectives in Biology

212

186

View full text Add to dashboard Cite

The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs. To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for L-amino acids, but did not completely exclude D-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.

show abstract

“…Additionally, diverse kinds of N-acylamino acids, such as L-and D-amino acids 23,24 and exotic peptides 26 have been used for the initiation to express Nterminal-modified peptides. In the combination of the above techniques with appropriate chemical reactions, unique macrocyclic peptides can be synthesized.…”

Section: 41mentioning

confidence: 99%

Flexizymes-facilitated Genetic Code Reprogramming Leading to the Discovery of Drug-like Peptides

Terasaka

Suga

2013

Chemistry Letters

Self Cite

View full text Add to dashboard Cite

Flexizymes are a family of aminoacylation ribozymes devised by in vitro selection in our research group. They charge a wide variety of nonproteinogenic amino acids onto virtually any kind of tRNAs, enabling us to reprogram the genetic code in a custom-made cell-free translation system. This genetic code reprogramming method was integrated with a mRNA display method, which not only expresses nonstandard peptides such as macrocyclic peptides but also selects ligands specifically binding to target proteins. This system is referred to as random nonstandard peptide integrated discovery (RaPID) system, which has yielded inhibitors against disease-related target proteins. In this review, we summarize the evolutionary history and recent applications of the flexizymes and RaPID system.

show abstract

Initiating translation with D-amino acids

Cited by 115 publications

References 35 publications

Towards Reassignment of the Methionine Codon AUG to Two Different Noncanonical Amino Acids in Bacterial Translation

Towards Reassignment of the Methionine Codon AUG to Two Different Noncanonical Amino Acids in Bacterial Translation

Origin and Evolution of the Ribosome

Flexizymes-facilitated Genetic Code Reprogramming Leading to the Discovery of Drug-like Peptides

Contact Info

Product

Resources

About