Pyrrolysine Encoded by UAG in Archaea: Charging of a UAG-Decoding Specialized tRNA

  title={Pyrrolysine Encoded by UAG in Archaea: Charging of a UAG-Decoding Specialized tRNA},
  author={Gayathri Rajaram Srinivasan and Carey M. James and Joseph Adrian Krzycki},
  pages={1459 - 1462}
Pyrrolysine is a lysine derivative encoded by the UAG codon in methylamine methyltransferase genes of Methanosarcina barkeri. Near a methyltransferase gene cluster is thepylT gene, which encodes an unusual transfer RNA (tRNA) with a CUA anticodon. The adjacent pylS gene encodes a class II aminoacyl-tRNA synthetase that charges the pylT-derived tRNA with lysine but is not closely related to known lysyl-tRNA synthetases. Homologs of pylS and pylT are found in a Gram-positive bacterium. Charging a… 

Atypical archaeal tRNA pyrrolysine transcript behaves towards EF-Tu as a typical elongator tRNA.

Hydrolysis protection assays show that lysylated tRNA(Pyl) can be recognized by bacterial elongation factor, and indicates that no antideterminant sequence is present in the body of the tRNAs transcript to prevent it from interacting with EF-Tu, in contrast with the otherwise functionally similar t RNA(Sec) that mediates selenocysteine incorporation.

The direct genetic encoding of pyrrolysine.

  • J. Krzycki
  • Biology, Chemistry
    Current opinion in microbiology
  • 2005

Functional context, biosynthesis, and genetic encoding of pyrrolysine.

Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool.

tRNAPyl: Structure, function, and applications

The work that has been done to elucidate the structure of tRNAPyl, its interaction with PylRS, and survey recent progress on the use of t RNAPyl as a tool for genetic code expansion are examined.

Translation of UAG as Pyrrolysine

Pyrrolysine incorporation appears to occur to some extent by amber suppression on a genome-wide basis in methanogenic Archaea, and some methanogen genomes encode additional homologs of elongation and release factors, however, their limited distribution suggests at best a nonessential role in enhancing UAG translation as pyrrolesine.

Direct charging of tRNACUA with pyrrolysine in vitro and in vivo

This work establishes that synthetic l-pyrrolysine is attached as a free molecule to tRNACUA by PylS, an archaeal class II aminoacyl-tRNA synthetase, and shows that the genetic code of E. coli can be expanded to include UAG-directed pyr rolysine incorporation into proteins.

Pyrrolysine in archaea: a 22nd amino acid encoded through a genetic code expansion.

The article reviews the authors' knowledge of this fascinating exception to the 'standard' genetic code, pyrrolysine, and reveals wider presence in archaea, deepened functional understanding and remarkable carbon source-dependent expression of expanded decoding and extended exploitation of the pyr rolysine machinery for synthetic code expansion.



A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases.

The proposed amino acid sequence is similar to open reading frames of unassigned function in both Methanobacterium thermoautotrophicum and Methanococcus jannaschii but is unrelated to canonical LysRS proteins reported in eubacteria, eukaryotes, and the crenarchaeote Sulfolobus solfataricus.

Selenocysteine inserting tRNAs: an overview.

Although there are still some uncertainties concerning the precise secondary and tertiary structures of eukaryal tRNA(Sec), the major identity determinant for selenocysteine biosynthesis and insertion appears to be the 13 bp long extended acceptor arm.

Glutamyl-tRNA(Gln) amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis.

Examination of the preliminary genomic sequence of the radiation-resistant bacterium Deinococcus radiodurans suggests the presence of both direct and indirect routes of Asn-tRNA and Gln- tRNA formation, and suggests that the gatCAB genes may be responsible for biosynthesis ofAsparagine in this asparagine prototroph.

The Amber Codon in the Gene Encoding the Monomethylamine Methyltransferase Isolated from Methanosarcina barkeri Is Translated as a Sense Codon*

The amber codon is thus read through during translation at apparently high efficiency and corresponds to lysine in tryptic fragments of MtmB even though canonical lysinesine codon usage is encountered in otherMethanosarcina genes.

The crystal structures of T. thermophilus lysyl‐tRNA synthetase complexed with E. coli tRNA(Lys) and a T. thermophilus tRNA(Lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl‐adenylate analogue.

The crystal structures of Thermus thermophilus lysyl‐tRNA synthetase, a class IIb aminoacyl‐tRNA synthetase, complexed with Escherchia coli tRNA(Lys)(mnm5 s2UUU) at 2.75 A resolution and with a T.

Aminoacyl-tRNA synthesis.

Current knowledge of the biochemical, structural, and evolutionary facets of aminoacyl-tRNA synthesis is reviewed, mainly prompted by the advent of whole genome sequencing and the availability of vast body of structural data.

Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs

Surprisingly, this partition of aaRS in two classes is found to be strongly correlated on the functional level with the acylation occurring either on the 2′ OH or 3′ OH of the ribose of the last nucleotide of tRNA.

Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction.

Aminoacyl-tRNA synthetases play a key role in protein biosynthesis by catalyzing the specific aminoacylation of tRNA. The energy required for the formation of the ester bond between the amino acid

Substrate recognition by class I lysyl-tRNA synthetases: a molecular basis for gene displacement.

Genes encoding both an archaeal and a bacterial class I enzyme were able to rescue an Escherichia coli strain deficient in LysRS, indicating their ability to functionally substitute for a class II LysRS in vivo.

Clustered Genes Encoding the Methyltransferases of Methanogenesis from Monomethylamine

A mechanism that circumvents UAG-directed termination of translation must operate during expression of mtmB in this methanogen, as well as in methionine synthase.