Programmed Deviations of Ribosomes From Standard Decoding in Archaea

Abstract

Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.

Keywords: alpha-fucosidase; archaea; frameshifting; pyrrolysine; recoding; selenocysteine.

FIGURE 1

Recoding events. Stop-codon readthrough: a different meaning is assigned to a stop codon with the insertion of the unusual amino acids selenocysteine and pyrrolysine. Frameshifting (+1 and –1): produces two polypeptides from different reading frames of the same mRNA. Ribosome Hopping: synthesizes one protein from two open discontinuous reading frames.

FIGURE 2

Sec biosynthesis in the three domains of life. In Archaea, as well as in Eukarya, Sec is synthesized in three steps. First (1), SerRS acylates tRNASec with serine to generate Ser-tRNASec. Then (2) PSTK forms Sep-tRNASec, which is converted to Sec-tRNASec by SepSecS in the presence of selenophosphate produced by selenophosphate synthetase (SPS) (3). -[Se]: reduced Se species; -SerRS: seryl-tRNA synthetase; -SelD/SPS: selenophosphate synthetase; -SelA: bacterial Sec synthase; -PstK: seryl-tRNASec kinase; -SepSecS: O-phosphoseryl-tRNA:selenocysteyl-tRNA synthase.

FIGURE 3

Sec translation in the three domains. Model of Sec incorporation in Bacteria (top), Eukarya (middle), and Archaea (bottom). -3′-UTR: 3′-untranslated region; -L30: ribosomal protein L30; -SBP2: SECIS-binding protein 2; -SECIS: Sec insertion sequence; -SelB/aSelB/eSelB: Sec-specific elongation factor.

FIGURE 4

The Pyl insertion system (A). Pyl, synthesized by pylB, pylD, pylC, is charged on a specific tRNA (encoded by pylT) whose anticodon AUC recognizes UAG codons in a specific reaction catalyzed by PylRS (encoded PylSc). See text for details. Figures arranged from Brugère et al. (2018). Biosynthesis of Pyl (B). The complete biosynthesis pathway of L-pyrrolysine from two lysines catalyzed by PylB, PylC and PylD.

FIGURE 5

The α-L-fucosidase gene. (A) The N-terminal SSO11867 ORF (highlighted in green) is in the zero frame, the C-terminal SSO3060 ORF (highlighted in blue), for which only a fragment is shown, is in the –1 frame. The 40 bp region of overlap bertween the two ORFs is indicated with a light yellow rectangle. The slippery heptameric sequence is underlined with a red line. The rare codons CAC are indicated with a black square. The putative stem and loop region is indicated with blu arrows. (B) framefucA mutant gene (only a fragment is shown). The red arrows indicate the mutated nucleotides in the slippery sequence.

FIGURE 6

Putative mechanism of programmed –1 frameshifting. (A) Simultaneous P- and A-site slippage; (B) P-site slippage. The slippery heptameric sequence is indicated in red. Rare codons are underlined with yellow line.