Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea

Abstract

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.

Figure 1

Scheme of hydrogenotrophic methanogenesis involving Sec-containing proteins (orange); the Cys-containing isoforms are in white. CoM-S-S-CoB, heterodisulfide of coenzyme M and coenzyme B; Fd, ferredoxin; Fd_ox, oxidized Fd; Fd_red, reduced Fd; FDH, formate dehydrogenase; FMD, formyl-methanofuran dehydrogenase; Fru, F₄₂₀-reducing hydrogenase; F₄₂₀, (oxidized) 8-hydroxy-5-deazariboflavin derivative; F₄₂₀H₂, reduced coenzyme F₄₂₀; H₄MPT, tetrahydromethanopterin, HDR, heterodisulfide reductase; HS-CoB, coenzyme B (N-7-mercaptoheptanoyl-O-phospho-L-threonine); HS-CoM, coenzyme M (2-mercaptoethanesulfonic acid); MF, methanofuran; Vhu, F₄₂₀-nonreducing hydrogenase.

Figure 2

Scheme of methylotrophic methanogenesis. Methyl groups from methanol, TMA, DMA, and MMA are mobilized into metabolism by the action of a substrate-specific methyltransferase interacting with its cognate corrinoid protein in which the cofactor's cobalt ion cycles between methyl-Co(III) and Co(I) states. Methyltransferases that are pyrrolysyl-proteins are marked with an asterisk. The corrinoid cofactor is then demethylated by the action of a methylcobamide:CoM methyltransferase such as MtbA (for methylamines) or MtaA (for methanol). Adventitious oxidation can inactive the corrinoid proteins to the Co(II) state, which can be reductively reactivated by RamA (for methylamines) and possibly by RamA homologs for other pathways. Reducing equivalents in the form of hydrogen, F₄₂₀H₂, or Fd_red from the oxidation of methyl-CoM are used to reduce methanophenazine (MP) and subsequently CoM-S-S-CoB, thereby generating ATP via electron transport phosphorylation and the free HS-CoM and HS-CoB cofactors; CoM-S-S-CoB is then recycled by the reduction of methyl-CoM to methane. See Figure 1 for cofactor abbreviations.

Figure 3

Schematic representation of selenocysteine biosynthesis and incorporation in Archaea. 3′UTR, 3′-untranslated region; PSTK, seryl-tRNA^sec kinase, [Se], reduced Se-species; SelB, Sec-specific elongation factor; SepSecS, O-phosphoseryl-tRNA^sec:selenocysteine synthase; Ser, serine; Se-P, seleno(mono)phosphate; SerRS, seryl-tRNA synthetase; SPS, selenophosphate synthetase; see text for details.

Figure 4

Schematic representation of pyrrolysine incorporation into protein. The pylB, pylC, and pylD genes have been shown to enable pyrrolysine biosynthesis in E. coli, but their exact roles are unknown. A conceptual and speculative scheme is shown which is keeping with the activities of proteins in their respective proteins families. Lysine is likely to form the acyl of pyrrolysine, but may also be coupled to an early precursor which subsequently cyclizes after amide bond formation. Pyrrolysine is given entrance to the genetic code by PylS in Archaea, the equivalent in Bacteria are the products of the split gene pylSc and pylSn. The direct formation of pyl-tRNA^Pyl is likely followed by binding to the elongation factor used by the canonical amino acids, that is, EF-1α in Archaea. The common bacterial elongation factor EF-Tu can bind charged tRNA^Pyl both in vivo and in vitro. The recognition of pyl-tRNA^Pyl by non-specialized elongation factors underlies the relatively high level of UAG translation in a reporter gene such as uidA with an introduced amber codon in organisms having tRNA^Pyl, PylS, and pyrrolysine or an analog to charge tRNA^Pyl. The PYLIS is not essential for this level of translation, as shown by replacement of PYLIS in mtmB1, but may enhance UAG translation to some extent. This effect is unlikely to require the structure formed by PYLIS. See text for further details.