Ancestral archaea expanded the genetic code with pyrrolysine

Unconventional genetic code systems in archaea

“…In these cases, the pylSc sequences of these two archaeal lineages more closely resemble bacterial pylSc sequences in Acetohalobium arabaticum and Halarsenatibacter silvermanii , rather than those in archaea. Aligning with previously discovered similarities between the Pyl operon in A. arabaticum and archaea, the similarities between the pylSc of these archaeal and bacterial lineages further support the hypothesis of LGT of the Pyl operon from archaea to bacteria ( Borrel et al, 2014 ; Guo et al, 2022 ).…”

“…Recently, seven archaeal genomes have been found to encode the NTD and CTD as two distinct genes, pylSn and pylSc , as commonly seen in bacteria ( Figure 3A ; Guo et al, 2022 ). Two examples are the PylRS enzymes found in the Methanomicrobia archaeon JdFR-19 and Candidatus Hydrothermarchaeum profundi ( Guo et al, 2022 ).…”

“…Recently, seven archaeal genomes have been found to encode the NTD and CTD as two distinct genes, pylSn and pylSc , as commonly seen in bacteria ( Figure 3A ; Guo et al, 2022 ). Two examples are the PylRS enzymes found in the Methanomicrobia archaeon JdFR-19 and Candidatus Hydrothermarchaeum profundi ( Guo et al, 2022 ). In these cases, the pylSc sequences of these two archaeal lineages more closely resemble bacterial pylSc sequences in Acetohalobium arabaticum and Halarsenatibacter silvermanii , rather than those in archaea.…”

“…Some classes of PylRS enzymes also include an N-terminal RNA-binding domain that does not resemble any currently known protein domains ( Jiang and Krzycki, 2012 ; Wan et al, 2014 ). In archaea, PylRS is commonly encoded by a single pylS gene, whereas the CTD and NTD of all bacterial and certain archaeal PylRS are encoded by two separate genes, pylSn and pylSc ( Yuan et al, 2010b ; Guo et al, 2022 ). The PylRS enzymes found in archaea can be classified into three major classes: the PylSn-PylSc fusion class, the PylSn+PylSc class, and the ΔPylSn class ( Figure 3A ; Dunkelmann et al, 2020 ; Krahn et al, 2020 ; Guo et al, 2022 ).…”

“…Though the PylRS of JdFR-19 belongs to the PylSc+PylSn class, this archaeon is a closely related relative of the Methanosarcinaceae , which encodes PylRS of the PylSc-PylSn fusion class ( Guo et al, 2022 ). Another close relative to Methanosarcinaceae is the organism Methermicoccus shengliensis , which encodes the ΔPylSn class of PylRS ( Cheng et al, 2007 ).…”