Abstract
This chapter discusses four unique aspects of archaeal aa‐tRNA formation that led to a much deeper understanding of this process not only in the Archaea, but in all domains of life. The topics are: (i) processing of half‐tRNA genes to mature tRNA in Nanoarchaeum equitans, (ii) RNA‐dependent cysteine synthesis in methanogens, (iii) pyrrolysyl‐tRNA formation in the Methanosarcinaceae, and (iv) glutaminyl‐ tRNA synthesis in archaea. The bulge‐helix‐bulge (BHB) motifs postulated to form at the intron‐exon junctions of archaeal tRNAs show divergence from the canonical structure. Once mature tRNA has been generated each tRNA species needs to be acylated (charged) with the correct amino acid. This is primarily achieved by the direct attachment of an amino acid to the corresponding tRNA by an aminoacyl‐tRNA synthetase. However, since many organisms lack the complete set of 20 aminoacyl‐tRNA synthetases (aaRSs), many biochemical, genetic, and genomic studies revealed the existence of an essential indirect two‐step pathway that also provides correctly charged aa‐tRNA. The aminoacyl‐tRNA synthetases are an ancient family of enzymes that esterify an amino acid to the 3' end of the cognate tRNA species. The current understanding of the Methanothermobacter thermautotrophicus Glu‐tRNA
Gln
amidotransferase GatDE is discussed. Discovery of the tRNA‐dependent cysteine biosynthetic route in M. jannaschii may have implications that reach far beyond the only problem of the formation of Cys‐tRNA
Cys
in three methanogenic archaea. The Methanosarcinaceae are an exception among the methanogens, as they are able to use compounds like methanol, methylated thiols, and methylamines as energy sources.