Characterization of N-Linked Protein Glycosylation in Helicobacter pullorum

The first bacterial N-linked glycosylation system was discovered in Campylobacter jejuni, and the key enzyme involved in the coupling of glycan to asparagine residues within the acceptor sequon of the glycoprotein is the oligosaccharyltransferase PglB. Emerging genome sequence data have revealed that pglB orthologues are present in a subset of species from the Deltaproteobacteria and Epsilonproteobacteria, including three Helicobacter species: H. pullorum, H. canadensis, and H. winghamensis. In contrast to C. jejuni, in which a single pglB gene is located within a larger gene cluster encoding the enzymes required for the biosynthesis of the N-linked glycan, these Helicobacter species contain two unrelated pglB genes (pglB1 and pglB2), neither of which is located within a larger locus involved in protein glycosylation. In complementation experiments, the H. pullorum PglB1 protein, but not PglB2, was able to transfer C. jejuni N-linked glycan onto an acceptor protein in Escherichia coli. Analysis of the characterized C. jejuni N-glycosylation system with an in vitro oligosaccharyltransferase assay followed by matrix-assisted laser desorption ionization (MALDI) mass spectrometry demonstrated the utility of this approach, and when applied to H. pullorum, PglB1-dependent N glycosylation with a linear pentasaccharide was observed. This reaction required an acidic residue at the −2 position of the N-glycosylation sequon, as for C. jejuni. Attempted insertional knockout mutagenesis of the H. pullorum pglB2 gene was unsuccessful, suggesting that it is essential. These first data on N-linked glycosylation in a second bacterial species demonstrate the similarities to, and fundamental differences from, the well-studied C. jejuni system.Glycosylation is one of the most common protein modifications, and eukaryotes glycosylate many of their secreted proteins with asparagine or N-linked glycans. This process is thought to have diverse roles in protein folding, quality control, protein secretion, and sorting (13). Eukaryotic glycosylation takes place at the luminal side of the endoplasmic reticulum (ER) membrane, where a preassembled oligosaccharide is transferred from a lipid carrier to asparagine residues within an N-X-S/T consensus sequence, where X can be any amino acid except proline (19). The coupling of glycan to the protein takes place cotranslationally as nascent polypeptide chains cross the ER membrane via a translocon apparatus (5). This reaction involves a protein complex of at least eight subunits (49), with the STT3 protein (50, 52) apparently acting as the central enzyme in the process of N-linked protein glycosylation (29, 48). The STT3 protein consists of an amino terminus with multiple membrane-spanning domains and a carboxy-terminal region containing the highly conserved WWDYG amino acid sequence motif (15).The first prokaryotic glycoproteins were described for archaeal species over 30 years ago (26), and for some time it was thought that protein glycosylation was a eukaryotic and archaeal, but not a bacterial, trait. However, there are now many examples of protein glycosylation in species from the domain Bacteria. For example, general O-linked protein glycosylation systems in which functionally diverse sets of proteins are glycosylated via a single pathway have recently been identified in Neisseria and Bacteroides spp. (8, 21, 44). The most-well-characterized bacterial species with respect to protein glycosylation is the enteropathogen Campylobacter jejuni, which encodes an O-linked system that glycosylates the flagellin protein of the flagellar filament along with the first described bacterial N-linked glycosylation system (39).The C. jejuni N-linked glycosylation pathway is encoded by genes from a single protein glycosylation, or pgl, locus (38). The glycosylation reaction is thought to occur at the periplasmic face of the bacterial inner membrane mediated by the product of the STT3 orthologue pglB (46). The C. jejuni heptasaccharide glycan is assembled on a lipid carrier in the cytoplasm through the action of glycosyltransferases encoded by the pglA, pglC, pglH, pglJ, and pglI genes (11, 12, 24, 31). This lipid-linked oligosaccharide (LLO) is then “flipped” into the periplasm by the pglK gene product, or “flippase” (1), and transferred by PglB onto an asparagine residue within an extended D/E-X-N-X-S/T sequon (19). Many C. jejuni periplasmic and surface proteins of diverse function are N glycosylated (51), yet the function of glycosylation remains elusive. Unlike in eukaryotes, this process occurs posttranslationally, and the surface location of the sequon in folded proteins appears to be required for glycosylation (20).The C. jejuni pgl gene locus can be transferred into Escherichia coli, and the corresponding gene products will function to transfer the heptasaccharide onto asparagine residues of coexpressed C. jejuni glycoproteins as well as non-C. jejuni proteins containing the appropriately located acceptor sequon (19, 46). When alternative lipid-linked glycans are present, such as those involved in lipopolysaccharide biosynthesis, glycans with diverse structure can also be transferred onto proteins (7). Although there are limitations, particularly with regard to the apparent structural requirement for an acetamido group on the C-2 carbon of the reducing end sugar (7, 47), this is still a significant advance toward tractable in vivo systems for glycoconjugate synthesis. The identification and characterization of further bacterial PglB proteins with potentially diverse properties would considerably expand the utility of such systems. Data from genome sequencing indicate that pglB orthologues are found in species closely related to C. jejuni, such as Campylobacter coli, Campylobacter lari, and Campylobacter upsaliensis (40), as well as in the more distantly related species Wolinella succinogenes (2). These species are members of the phylogenetic grouping known as the epsilon subdivision of the Proteobacteria, or Epsilonproteobacteria, consisting of the well-established genera Campylobacter, Helicobacter, Arcobacter, and Wolinella, which are often associated with human and animal hosts, as well as a number of newly recognized groupings of environmental bacteria often found in sulfidic environments (3). However, not all species of Epsilonproteobacteria contain pglB orthologues, and until recently, all characterized Helicobacter species lacked pglB genes.Given the considerable interest in exploiting bacterial protein glycosylation, especially the C. jejuni N-linked glycosylation system, for generating glycoconjugates of biotechnological and therapeutic potential, the functional characterization of newly discovered pglB orthologues is a priority. In this report we describe the application of an in vitro oligosaccharyltransferase assay to investigate N-linked glycosylation initially in C. jejuni, where the utility of this approach was demonstrated, and then in Helicobacter pullorum, demonstrating that one of the two H. pullorum PglB enzymes is responsible for N-linked protein glycosylation with a pentasaccharide glycan.     

The species–area relationship in centipedes (Myriapoda: Chilopoda): a comparison between Mediterranean island groups

The present study article examines the shapes of centipede species–area relationships (SARs) in the Mediterranean islands, compares the results of the linear form of the power model between archipelagos, discusses biological significance of the power model parameters with other taxa on the Aegean archipelago, and tests for a significant small‐island effect (SIE). We used 11 models to test the SARs and we compared the quality‐of‐fit of all candidate models. The power function ranked first and Z‐values was in the range 0.106–0.334. We assessed the presence of SIEs by fitting both a continuous and discontinuous breakpoint regression model. The continuous breakpoint regression functions never performed much better than the closest discontinuous model as a predictor of centipede species richness. We suggest that the relatively low Z‐values in our data partly reflect better dispersal abilities in centipedes than in other soil invertebrate taxa. Longer periods of isolation and more recent island formation may explain the somewhat lower constant c in the western Mediterranean islands compared to the Aegean islands. Higher breakpoint values in the western Mediterranean may also be a result of larger distance to the mainland and longer separation times. Despite the differences in the geological history and the idiosyncratic features of the main island groups considered, the overall results are quite similar and this could be assigned to the ability of centipedes to disperse across isolation barriers. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 146–159.     

Use of the Gram stain in microbiology

The Gram stain differentiates bacteria into two fundamental varieties of cells. Bacteria that retain the initial crystal violet stain (purple) are said to be 'Gram-positive,' whereas those that are decolorized and stain red with carbol fuchsin (or safranin) are said to be 'Gram-negative.' This staining response is based on the chemical and structural makeup of the cell walls of both varieties of bacteria. Gram-positives have a thick, relatively impermeable wall that resists decolorization and is composed of peptidoglycan and secondary polymers. Gram-negatives have a thin peptidoglycan layer plus an overlying lipid-protein bilayer known as the outer membrane, which can be disrupted by decolorization. Some bacteria have walls of intermediate structure and, although they are officially classified as Gram-positives because of their linage, they stain in a variable manner. One prokaryote domain, the Archaea, have such variability of wall structure that the Gram stain is not a useful differentiating tool.     

Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs

Presence of the dihydrouridine (D) stem in the mitochondrial cysteine tRNA is unusually variable among lepidosaurian reptiles. Phylogenetic and comparative analyses of cysteine tRNA gene sequences identify eight parallel losses of the D-stem, resulting in D-arm replacement loops. Sampling within the monophyletic Acrodonta provides no evidence for reversal. Slipped-strand mispairing of noncontiguous repeated sequences during replication or direct replication slippage can explain repeats observed within cysteine tRNAs that contain a D-arm replacement loop. These two mechanisms involving replication slippage can account for the loss of the cysteine tRNA D-stem in several lepidosaurian lineages, and may represent general mechanisms by which the secondary structures of mitochondrial tRNAs are altered.