SummaryArchaea, one of three major evolutionary lineages of life, encode proteasomes highly related to those of eukaryotes. In contrast, archaeal ubiquitin-like proteins are less conserved and not known to function in protein conjugation. This has complicated our understanding of the origins of ubiquitination and its connection to proteasomes. Here we report two small archaeal modifier proteins, SAMP1 and SAMP2, with a β-grasp fold and C-terminal diglycine motif similar to ubiquitin, that form protein-conjugates in the archaeon Haloferax volcanii. SAMP-conjugates were altered by nitrogen-limitation and proteasomal gene knockout and spanned various functions including components of the Urm1 pathway. LC-MS/MS-based collision-induced dissociation demonstrated isopeptide bonds between the C-terminal glycine of SAMP2 and the ε-amino group of lysines from a number of protein targets and Lys58 of SAMP2 itself, revealing poly-SAMP chains. The widespread distribution and diversity of pathways modified by SAMPylation suggest this type of protein-conjugation is central to the archaeal lineage.

The structural diversity of glycoprotein N-linked oligosaccharides is determined by the expression and regulation of glycosyltransferase activities and by the availability of the appropriate acceptor/donor substrates. Cells in different tissues and in different developmental stages utilize these control points to manifest unique glycan expression patterns in response to their surroundings. The activity of a Toll-like receptor, called Tollo/ Toll-8, induces a pattern of incompletely defined, but neural specific, glycan expression in the Drosophila embryo. Understanding the full extent of the changes in glycan expression that result from altered Tollo/Toll-8 signaling requires characterization of the complete N-linked glycan profile of both wild-type and mutant embryos. N-Linked glycans harvested from wildtype or mutant embryos were subjected to direct structural analysis by analytic and preparative high pressure liquid chromatography, by multidimensional mass spectrometry, and by exoglycosidase digestion, revealing a predominance of high mannose and paucimannose glycans. Di-, mono-, and nonfucosylated forms of hybrid, complex biantennary, and triantennary glycans account for 12% of the total wild-type glycan profile. Two sialylated glycans bearing N-acetylneuraminic acid were detected, the first direct demonstration of this modification in Drosophila. Glycan profiles change during normal development consistent with increasing ␣-mannosidase II and core fucosyltransferase enzyme activities, and with decreasing activity of the Fused lobes processing hexosaminidase. In tollo/toll-8 mutants, a dramatic, expected loss of difucosylated glycans is accompanied by unexpected decreases in monofucosylated and nonfucosylated hybrid glycans and increases in some nonfucosylated paucimannose and biantennary glycans. Therefore, tollo/toll-8 signaling influences flux through several processing steps that affect the maturation of N-linked glycans.Cell surface glycans mediate interactions between cells and define cellular identities within complex tissues at all stages of life (1-6). As embryonic cells differentiate and form organized tissues, glycan expression diversifies, generating glycosylation profiles that are specific for tissue and cell type (7-9). Mutations that affect oligosaccharide synthesis or processing result in neural deficits, skeletal/connective tissue abnormalities, anemia, compromised immune response, muscular dystrophy, or generalized failure to thrive (10 -14). The vital functions of cellular glycans and the pathophysiologic consequences of altered glycosylation emphasize the need for understanding the basic mechanisms that regulate glycan expression in intact organisms.The expanding characterization of glycosyltransferases in Drosophila melanogaster has begun to define the bounds of structural diversity in the glycan portfolio of the organism and has also generated new opportunities for genetically dissecting the mechanisms that control glycosylation. Loss-of-function mutations have been described in a handful...

In Caenorhabditis elegans, the Gli-family transcription factor TRA-1 is the terminal effector of the sex-determination pathway. TRA-1 activity inhibits male development and allows female fates. Genetic studies have indicated that TRA-1 is negatively regulated by the fem-1, fem-2, and fem-3 genes. However, the mechanism of this regulation has not been understood. Here, we present data that TRA-1 is regulated by degradation mediated by a CUL-2-based ubiquitin ligase complex that contains FEM-1 as the substrate-recognition subunit, and FEM-2 and FEM-3 as cofactors. CUL-2 physically associates with both FEM-1 and TRA-1 in vivo, and cul-2 mutant males share feminization phenotypes with fem mutants. CUL-2 and the FEM proteins negatively regulate TRA-1 protein levels in C. elegans. When expressed in human cells, the FEM proteins interact with human CUL2 and induce the proteasome-dependent degradation of TRA-1. This work demonstrates that the terminal step in C. elegans sex determination is controlled by ubiquitin-mediated proteolysis.

Congenital muscular dystrophy (CMD) 3 is a heterogeneous group of inherited neuromuscular disorders characterized by severe muscle weakness, ocular and neuronal migration abnormalities, and variable mental retardation (1). Within recent years, it has become increasing clear through genetic studies that hypoglycosylation of the protein dystroglycan (DG) is a commonality in many forms of CMD (the so-called dystroglycanopathies). DG is post-translationally cleaved into an extracellular ␣-DG subunit and a transmembrane ␤-DG subunit (2). ␣-DG is a key component of the dystrophin-glycoprotein complex that serves as a link between the cytoskeleton of cells and the extracellular matrix by binding to proteins such as laminin (3). Interaction between ␣-DG and its extracellular ligands requires ␣-DG to be properly post-translationally modified through the addition of O-linked oligosaccharides, specifically O-mannose (4, 5). To date, mutations in six genes that encode determined or predicted glycosyltransferases have been shown to result in varying forms of CMD in which the post-translational processing of ␣-DG is affected (4 -6). The six mutated genes and their original resulting form of CMD are as follows: POMT1 (protein O-mannosyltransferase 1) and POMT2, Walker-Warburg syndrome (7,8); POMGnT1 (protein Olinked mannose ␤1,2-N-acetylglucosaminyltransferase 1), muscle-eye-brain disease (9); fukutin, Fukuyama congenital muscular dystrophy (10); FKRP (fukutin-related protein), congenital muscular dystrophy 1C (11); and LARGE, congenital muscular dystrophy 1D (12). Recent work has demonstrated that selected mutations in some of these genes can cause various forms of CMD that are likely dependent on the severity of the mutation on enzymatic activity and stability (13). Abnormal glycosylation of ␣-DG appears to be a commonality among all of the aforementioned forms of CMD. Although expression of ␣-DG appears not to be grossly affected, the ability of ␣-DG to be recognized by monoclonal antibodies IIH6 and VIA4 1 is eliminated, as is the ability of ␣-DG to properly bind its ligands (14).␣-DG is composed of a central mucin-like region that is extensively heterogeneously glycosylated with glycan chains that are initiated by both O-

Robust quantification is an essential component of comparative –omic strategies. In this regard, glycomics lags behind proteomics. Although various isotope-tagging and direct quantification methods have recently enhanced comparative glycan analysis, a cell culture labeling strategy, that could provide for glycomics the advantages that SILAC provides for proteomics, has not been described. Here we report the development of IDAWG, Isotopic Detection of Aminosugars With Glutamine, for the incorporation of differential mass tags into the glycans of cultured cells. In this method, culture media containing amide-15N-Gln is used to metabolically label cellular aminosugars with heavy nitrogen. Because the amide side chain of Gln is the sole source of nitrogen for the biosynthesis of GlcNAc, GalNAc, and sialic acid, we demonstrate that culturing mouse embryonic stems cells for 72 hours in the presence of amide-15N-Gln media results in nearly complete incorporation of 15N into N-linked and O-linked glycans. The isotopically heavy monosaccharide residues provide additional information for interpreting glycan fragmentation and also allow quantification in both full MS and MS/MS modes. Thus, IDAWG is a simple to implement, yet powerful quantitative tool for the glycomics toolbox.