Many archaeal proteins undergo posttranslational modifications. S-layer proteins and flagellins have been used successfully to study a variety of these modifications, including N-linked glycosylation, signal peptide removal and lipid modification. Use of these well-characterized reporter proteins in the genetically tractable model organisms, Haloferax volcanii, Methanococcus voltae and Methanococcus maripaludis, has allowed dissection of the pathways and characterization of many of the enzymes responsible for these modifications. Such studies have identified archaeal-specific variations in signal peptidase activity not found in the other domains of life, as well as the enzymes responsible for assembly and biosynthesis of novel N-linked glycans. In vitro assays for some of these enzymes have already been developed. N-linked glycosylation is not essential for either Hfx. volcanii or the Methanococcus species, an observation that allowed researchers to analyze the role played by glycosylation in the function of both S-layers and flagellins, by generating mutants possessing these reporters with only partial attached glycans or lacking glycan altogether. In future studies, it will be possible to consider questions related to the heterogeneity associated with given modifications, such as differential or modulated glycosylation. 1. Introduction Carl Woese initially defined the third form of life, the Archaea, on the basis of the novel oligonucleotide signatures of their small ribosomal subunit RNA [1–3]. Specifically, by generating phylogenetic trees based on 16S rRNA sequences, Woese clearly showed that Archaea formed a unique group, distinct from Bacteria or Eukarya. However, early analysis also revealed that this unusual group of microbes shared a variety of other characteristics, most notably ether-linked membrane lipids, a variety of unusual cell walls (none of which contained murein), atypical DNA-dependent RNA polymerases and later, their own variation of flagella [4, 5]. Indeed, cell wall composition was one of the very first phenotypical traits of the Archaea considered that allowed for differentiation from Bacteria [6] and was considered in the early days of archaeal research to be “the only useful phylogenetic criterion, other than direct molecular phylogenetic measurement” to distinguish between the two prokaryotic domains [7]. A common feature of many genera of Archaea, found in representatives of all the major lineages, is the presence of an outermost component of the cell envelope termed the surface (S)-layer, comprising protein or often
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