Unconventional genetic code systems in archaea

Abstract

Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.

Keywords: archaea; genetic code expansion; phosphoserine; pyrrolysine; selenocysteine.

Figure 1

Selenocysteine (Sec) biosynthesis pathways in all domains of life. (A) In bacteria, the conversion of serine (Ser) to Sec occurs through a single step catalyzed by selenocysteine synthase (SelA), after tRNA^Sec is aminoacylated by seryl-tRNA synthetase (SerRS). Sec is then incorporated at UGA codons with an immediate downstream selenocysteine insertion sequence (SECIS) element. In (B) eukaryotes and (C) archaea, two steps are needed to synthesize Sec from Ser, through the activity of phosphoseryl-tRNA^Sec kinase (PSTK) and O-phosphoseryl-tRNA^Sec:Sec synthase (SepSecS). The 3′-untranslated region (UTR), which contains the SECIS element, bends to position the mRNA element closer to the UGA codon. The factors mediating this recruitment are not fully known in archaea and eukaryotes. In all three domains, a Sec-specific elongation factor (SelB in bacteria, aSelB in archaea, and EFSec in eukaryotes) functions to bring Sec-tRNA^Sec to the ribosome.

Figure 2

tRNA^Sec secondary structures across all domains of life. Small but conserved differences are observed between (A) bacterial, (B) archaeal, and (C) eukaryotic tRNA^Sec. While canonical archaeal and eukaryotic tRNA^Sec share the post-transcriptionally added CCA tail and the 9/4 configuration of the acceptor stem (green) and T-arm (dark blue), archaeal tRNA^Sec possesses a longer D-arm (light blue) than both bacterial and eukaryotic tRNA^Sec. The tRNA^Sec for all three domains share the G73 discriminator base as an identity element (outlined in yellow), but eukaryotic tRNA^Sec also has a conserved U6:U67 base pair. Note that exceptions to the canonical archaeal tRNA^Sec shown in this figure have been reported.

Figure 3

PylRS domain architectures and tRNA^Pyl secondary structures in archaea. (A) Domains of the PylRS genes from the different enzyme classes highlight the lack of an N-terminal domain for the class A and class B ΔNPylRS and the encoding of the CTD and NTD of PylRS in separate genes for the PylSc+PylSn class. tRNA^Pyl secondary structures recognized by (B) PylSc-PylSn fusion class PylRS, (C) class A ΔNPylRS, and (D) class B ΔNPylRS (Dunkelmann et al., 2020). The identity elements for all three classes of tRNA^Pyl molecules are outlined in yellow. The tRNA^Pyl recognized by class A and B ΔNPylRS (tRNA^ΔNPyl) noticeably contain a break or bulge in the anticodon stem (pink). For the class A tRNA^ΔNPyl, nucleotides highlighted in red represent bases that are missing in the sequence of other class A tRNA^ΔNPyl, whereas circles without nucleotides represent those that are missing in the Ca. M. alvus sequence but present in others of the same class.

Figure 4

tRNA-dependent biosynthesis of amino acids in archaea. (A) Schematic of the traditional tRNA-independent biosynthesis of amino acids, (B) cysteine (Cys), (C) glutamine (Gln), and (D) asparagine (Asn) proceed through different mechanisms. (B) Protein complex formation precedes binding of tRNA^Cys. The two-step process of Cys biosynthesis occurs through O-phosphoseryl-tRNA synthetase (SepRS) and SepCysS, while the protein-tRNA^Cys complex remains intact until phosphoseryl is converted to Cys. (C) tRNA-dependent Gln biosynthesis also begins with protein complex formation followed by binding of tRNA^Gln. After non-discriminating glutamyl-tRNA synthetase (ND-GluRS) aminoacylates tRNA^Gln with glutamic acid (Glu), ND-GluRS dissociates for the GatDE heterodimer to catalyze the conversion of Glu to Gln. (D) Non-discriminating aspartyl-tRNA synthetase (ND-AspRS) and GatCAB form a complex through binding tRNA^Asn. This complex remains intact even after ND-AspRS aminoacylates tRNA^Asn with aspartic acid (Asp), and the complex only dissociates once GatCAB converts Asp to Asn. In all pathways, archaeal EF-1α brings the aminoacyl-tRNAs (aa-tRNAs) to the ribosome.

Figure 5

Summary of the genetic code systems found in various archaeal lineages. Lineages positioned within a section possess the complete machinery for the designated system, while those located on the border of a section possess only partial machinery. An asterisk (*) indicates that only certain species within the lineage utilize the specified system. All archaea utilize the tRNA-dependent Gln biosynthesis system. Gln, glutamine; Sec, selenocysteine; Pyl, pyrrolysine; Cys, cysteine; Asn, asparagine; TMCG, Terrestrial Miscellaneous Crenarchaeota group; HMET1, Candidatus Methanohalarchaeum thermophilum HMET1; JdFR-19, Methanomicrobia archaeon JdFR-19; MSBL1, Mediterranean Sea Brine Lakes 1 archaeon SCGC-AAA382A20.