Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. This paper highlights these differences and summarizes the recent developments in selenocysteine- and pyrrolysine-related research on archaea and aims to put this knowledge into the context of their unique energy metabolism. 1. Introduction Expansion of the amino acid repertoire of proteins beyond the 20 “canonical” amino acids is a phenomenon observed almost 50 years ago [1]. Numerous modifications of the carboxyl- or amino-terminals or the individual side chains of amino acids after ribosomal synthesis of the respective polypeptide had finished were identified and the biosynthetic path elucidated (reviewed in [2]). It is thus not surprising that a similar process was assumed when selenocysteine, 2-selenoalanine, was discovered as constituent of eukaryal and bacterial proteins [3]. What made selenocysteine special is that subsequent efforts established the cotranslational nature of its insertion into proteins at the position of a UGA stop codon on the respective mRNA [4, 5]. Thus, selenocysteine was designated the 21st proteinogenic amino acid [6]. Discovery of pyrrolysine, lysine with in amide linkage to (4R,5R)-4-methyl-pyrroline-5-carboxylate, occurred in a different order, a single in-frame amber codon within the gene encoding the monomethylamine (MMA) methyltransferase in Methanosarcina barkeri [7, 8] was later found to correspond to pyrrolysine in the crystal structure [9, 10] and have its own tRNA [11]. As pyrrolysine was also shown to be inserted cotranslationally, it was designated the 22nd proteinogenic amino acid [10]. Beside the fact that translation of selenocysteine and pyrrolysine both involves suppression of stop codons the two systems have little in common (also reviewed in [12, 13]). To emphasize the differences between the mechanisms underlying selenocysteine and pyrrolysine translation, to summarize recent insights from efforts to better understand the biology of these two unusual amino acids, and to put this knowledge into the physiological
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