Recoding in Archaea

Abstract

SummaryStandard decoding of the genetic information into polypeptides is performed by one of the most sophisticated cell machineries, the translating ribosome, which, by following the genetic code, ensures the correspondence between the mature mRNA and the protein sequence. However, the expression of a minority of genes requires programmed deviations from the standard decoding rules, globally named recoding . This includes ribosome programmed -/ + 1 frameshifting, ribosome hopping, and stop codon readthrough. Recoding in Archaea was unequivocally demonstrated only for the translation of the UGA stop codon into the amino acid selenocysteine. However, a new recoding event leading to the 22nd amino acid pyrrolysine and the preliminary reports on a gene regulated by programmed ----1 frameshifting have been recently described in Archaea. Therefore, it appears that the study of this phenomenon in Archaea is still at its dawn and that most of the genes whose expression is regulated by recoding are still uncharacterized.

Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects

“…These authors describe a mechanism in which the RNA chain dissociates from the DNA template and reassociates in a new location. Third, functional proteins may be restored by frameshifting during translation, or "recoding," a phenomenon that occurs in yeast (Hansen et al 2003), archea (Cobucci-Ponzano et al 2005), and E. coli and can also follow poly(A) tracts, especially in the form of A_AAA_AAG (Baranov et al 2002. Such slippage has been proposed to explain aberrant indels in animal mitochondrial genes (Beckenbach et al 2005), and in principle, might operate in endosymbionts.…”

Characterization of the Archaeal ThermophileSulfolobusTurreted Icosahedral Virus Validates an Evolutionary Link among Double-Stranded DNA Viruses from All Domains of Life

“…3). Recoding of genetic information is well documented in archaea, including the use of nonstandard amino acids, frameshifts, read-through of amber codons, and alternative sites for the initiation of transcription (12,26). To assure that virally expressed proteins were not overlooked, we reformatted our protein sequence database such that ORFs began immediately after stop codons and allowed for read-through products of the amber codon.…”

“…Chlorine atoms are a mixture of two isotopes, 35 Cl and 37 Cl, with abundances of 75.8 and 25.2%, respectively. The isotopic pattern of lipids is dominated by 12 C and 13 C, with abundances of 98.9 and 1.1%, respectively. The presence of a chlorine atom alters the isotopic distribution, and therefore the observed ratio can be used to distinguish between neutral and acidic lipids (33).…”

“…Protein identifications were based on peptide mass and fragmentation pattern matches in the NCBInr database and an in-house database that contained the STIV genome translated in all six reading frames and the complete genome of S. solfataricus P2. The in-house database contained all ORFs greater than 24 nucleotides in the STIV genome and also included a pyrrolysine codon in place of the amber stop codon (12,24,26). In-gel digestion and nanospray MS/MS analysis using both an ion trap and Q-TOF instruments led to the identification of nine STIV-encoded proteins ( Table 1).…”

Gene decay in archaea

“…For the comparisons of the three Methanosarcina spp., it was necessary to disable this feature for the amber stop codon TAG, which instead codes for pyrrolysine in this genus (James et al 2001). In addition, all pseudogenes were curated manually for known recoding events (Cobucci-Ponzano et al 2005). Pseudogenes detected by the comparative analysis of full genome sequences can be either positional homologs or nonpositional homologs of CDSs in the reciprocal genomes, based on gene context conservation: positional pseudogenes are those that share at least one neighboring gene with the corresponding functional copy in the related genome.…”