6427006
Functional characterization of Ost3p. Loss of the 34-kD subunit of the Saccharomyces cerevisiae oligosaccharyltransferase results in biased underglycosylation of acceptor substrates
Within the lumen of the rough endoplasmic reticulum, oligosaccharyltransferase catalyzes the en bloc transfer of a high mannose oligosaccharide moiety from the lipid-linked oligosaccharide donor to asparagine acceptor sites in nascent polypeptides. The Saccharomyces cerevisiae oligosaccharyltransferase was purified as a heteroligomeric complex consisting of six subunits (alpha-zeta) having apparent molecular masses of 64 kD (Ost1p), 45 kD (Wbp1p), 34 kD, 30 kD (Swp1p), 16 kD, and 9 kD. Here we report a structural and functional characterization of Ost3p which corresponds to the 34-kD gamma-subunit of the oligosaccharyltransferase. Unlike Ost1p, Wbp1p, and Swp1p, expression of Ost3p is not essential for viability of yeast. Instead, ost3 null mutant yeast grow at wild-type rates on solid or in liquid media irrespective of culture temperature. Nonetheless, detergent extracts prepared from ost3 null mutant membranes are twofold less active than extracts prepared from wild-type membranes in an in vitro oligosaccharyltransferase assay. Furthermore, loss of Ost3p is accompanied by significant underglycosylation of soluble and membrane- bound glycoproteins in vivo. Compared to the previously characterized ost1-1 mutant in the oligosaccharyltransferase, and the alg5 mutant in the oligosaccharide assembly pathway, ost3 null mutant yeast appear to be selectively impaired in the glycosylation of several membrane glycoproteins. The latter observation suggests that Ost3p may enhance oligosaccharide transfer in vivo to a subset of acceptor substrates.
24628065
Glycoprotein biosynthesis in yeast
Many proteins in the yeast Saccharomyces cerevisiae are modified by the attachment of N‐linked saccharides to asparagine, of O‐linked mannose glycans to serine or threonine, and of glycosylphosphoinositol membrane anchors. The biosynthetic events leading to these modifications are coupled to the secretory pathway. Early stages of N‐linked glycosylation and the formation of glycosylphosphoinositol anchors have been conserved through evolution of eukaryotes. Studies of yeast offer a variety of genetic and molecular biological approaches, which have led to the isolation of different glycosylation mutants and of genes for enzymes involved in glycosylation. Yeast mutants are useful to identify biosynthetic intermediates, to establish whether a given enzyme is essential for viability, and to determine how cellular functions are affected when glycosylation is perturbed. Yeast glycosylation mutants and genes can be used to identify their counterparts in other eukaryotes.—Herscovics, A.; Orlean, P. Glycoprotein biosynthesis in yeast. FASEB J. 7: 540‐550; 1993.
11513312
Assembly of asparagine-linked oligosaccharides.
PERSPECTIVES AND SUMMARY 631 STRUCTURES OF ASPARAGINE-LINKED OLIGOSACCI-IARIDES 632 ASSEMBLY AND TRANSFER OF THE LIPID-LINKED OLIGOSACCHARIDE ...... 635 Assembly 635 Transfer-Oligosaccharide Structural Requirements 636 Transfer-Role of Peptide Acceptor 637 OLIGOSACCHARIDE P OCESSING 639 Sequence of Processing 639 Subcellular Localization of Processing Enzymes 641 Processing in Lower Organisms 643 Specificity of Processing Enzymes 644 OTHER POS’VI~RANSLATIONAL MODIFICATIONS 653 CONTROL F OLIGOSACCHARIDE PROCESSING 655
2554851
Biological roles of oligosaccharides: all of the theories are correct
Abstract Many different theories have been advanced concerning the biological roles of the oligosaccharide units of individual classes of glycoconjugates. Analysis of the evidence indicates that while all of these theories are correct, exceptions to each can also be found. The biological roles of oligosaccharides appear to span the spectrum from those that are trivial, to those that are crucial for the development, growth, function or survival of an organism. Some general principles emerge. First, it is difficult to predict a priori the functions a given oligosaccharide on a given glycoconjugate might be mediating, or their relative importance to the organism. Second, the same oligosaccharide sequence may mediate different functions at different locations within the same organism, or at different times in its ontogeny or life cycle. Third, the more specific and crucial biological roles of oligosaccharides are often mediated by unusual oligosaccharide sequences, unusual presentations of common terminal sequences, or by further modifications of the sugars themselves. However, such oligosaccharide sequences are also more likely to be targets for recognition by pathogenic toxins and microorganisms. As such, they are subject to more intra- and inter-species variation because of ongoing host—pathogen interactions during evolution. In the final analysis, the only common features of the varied functions of oligosaccharides are that they either mediate ‘specific recognition’ events or that they provide ‘modulation’ of biological processes. In so doing, they generate much of the functional diversity required for the development and differentiation of complex organisms, and for their interactions with other organisms in the environment.
25041487
Temperature-sensitive yeast mutants deficient in asparagine-linked glycosylation.
A [3H]mannose suicide selection has been used to isolate mutants in yeast which contain temperature-sensitive defects in asparagine-linked glycosylation. The surviving cells were screened at the nonpermissive temperature for a decreased ability to incorporate [3H]mannose and for defects in glycosylation of the secreted protein invertase. One of these mutants (alg1-1) has been characterized and found to be blocked in the assembly of the lipid-linked oligosaccharide precursor. The alg1-1 cells synthesize mannosyl compounds at 60% of the wild type level at the nonpermissive temperature and 105% of the wild type level at the permissive temperature. In vivo labeling experiments have demonstrated that alg1-1 cells are able to synthesize GlcNAc2-lipid but are unable to synthesize any mannose-containing oligosaccharide-lipids. This result was confirmed by in vitro labeling of yeast membranes. When incubated with UDP-[3H]GlcNAc, alg1-1 membranes synthesized GlcNAc2-lipid but failed to elongate it when GDP-Man was added. The alg1-1 membranes also failed to elongate exogenous GlcNAc2-lipid but were able to convert Man1GlcNAc2-lipid to Man5-Glc-NAc2-lipid in the presence of GDP-Man. These results indicate that the alg1-1 mutant is blocked specifically in the addition of the first mannose residue to the lipid-linked oligosaccharide precursor.
46304250
Oligosaccharyltransferase activity is associated with a protein complex composed of ribophorins I and II and a 48 kd protein
Oligosaccharyltransferase catalyzes the N-linked glycosylation of asparagine residues on nascent polypeptides in the lumen of the rough endoplasmic reticulum (RER). A protein complex composed of 66, 63, and 48 kd subunits copurified with oligosaccharyltransferase from canine pancreas. The 66 and 63 kd subunits were shown by protein immunoblotting to be identical to ribophorin I and II, two previously identified RER glycoproteins that colocalize with membrane-bound ribosomes. The transmembrane segment of ribophorin I was found to be homologous to a recently proposed dolichol recognition consensus sequence. Based on a revision of the consensus sequence, we propose a model for the interaction of dolichol with the glycosyltransferases that catalyze the assembly and transfer of lipid-linked oligosaccharides.
26034334
The 48-kDa subunit of the mammalian oligosaccharyltransferase complex is homologous to the essential yeast protein WBP1.
Oligosaccharyltransferase has been purified from canine microsomal membranes as a protein complex with three nonidentical subunits of 66, 63/64, and 48 kDa. The 66- and 63/64-kDa subunits were found to be identical to ribophorins I and II, respectively. The ribophorins are integral membrane glycoproteins that were previously shown to be localized exclusively to the rough endoplasmic reticulum. The 48-kDa subunit (OST48) of the oligosaccharyltransferase complex is not a glycoprotein and is not recognized by antibodies to either ribophorin. Here, we describe the characterization of a cDNA clone that encodes OST48. Like ribophorins I and II, OST48 was found to be an integral membrane protein, with the majority of the polypeptide located within the lumen of the endoplasmic reticulum. OST48 does not show significant amino acid sequence homology to either ribophorin I or II. A 45-kDa integral membrane protein, designated WBP1, from the yeast Saccharomyces cerevisiae was found to be 25% identical in sequence to OST48. Recently, WBP1 was shown to be essential for in vivo and in vitro expression of oligosaccharyltransferase activity in yeast. We conclude that OST48 and WBP1 are homologous gene products.
23172258
The yeast WBP1 is essential for oligosaccharyl transferase activity in vivo and in vitro.
Asparagine‐linked N‐glycosylation is a highly conserved and functionally important modification of proteins in eukaryotic cells. The central step in this process is a cotranslational transfer of lipid‐linked core oligosaccharides to selected Asn‐X‐Ser/Thr‐sequences of nascent polypeptide chains, catalysed by the enzyme N‐oligosaccharyl transferase. In this report we show that the essential yeast protein WBP1 (te Heesen et al., 1991) is required for N‐oligosaccharyl transferase in vivo and in vitro. Depletion of WBP1 correlates with a defect in transferring core oligosaccharides to carboxypeptidase Y and proteinase A in vivo. In addition, in vitro N‐glycosylation of the acceptor peptide Tyr‐Asn‐Leu‐Thr‐Ser‐Val using microsomal membranes from WBP1 depleted cells is reduced as compared with membranes from wild‐type cells. We propose that WBP1 is an essential component of the oligosaccharyl transferase in yeast.
24733962
The Saccharomyces cerevisiae oligosaccharyltransferase is a protein complex composed of Wbp1p, Swp1p, and four additional polypeptides.
Asparagine-linked glycosylation of proteins in the lumen of the endoplasmic reticulum is catalyzed by the oligosaccharyltransferase. Previously, the mammalian oligosaccharyltransferase was shown to co-purify with a protein complex consisting of three integral membrane proteins: ribophorin I and ribophorin II and a nonglycosylated 48-kDa polypeptide designated OST48. Here, we describe the purification of the oligosaccharyltransferase from Saccharomyces cerevisiae. The yeast oligosaccharyltransferase complex is composed of six subunits (alpha, beta, gamma, delta, epsilon, and zeta). The alpha subunit of the yeast oligosaccharyltransferase complex is a heterogeneously glycosylated protein with three glycoforms of 64, 62, and 60 kDa that contain, respectively, four, three, and two asparagine-linked oligosaccharide chains. The beta and delta subunits were shown to correspond to the 45-kDa Wbp1 glycoprotein and the 30-kDa Swp1 protein, respectively. The Wbp1 and Swp1 proteins were previously shown to be essential for asparagine-linked glycosylation in vivo. The nonglycosylated gamma, epsilon, and zeta subunits have apparent molecular masses of 34, 16, and 9 kDa. Homology between the yeast and mammalian oligosaccharyltransferase complexes first became evident when the 48-kDa subunit of the mammalian enzyme was found to be 25% identical in sequence with the Wbp1 protein. Here we present an alignment between the Swp1 protein and the carboxyl-terminal half of human ribophorin II that reveals that these two proteins are related gene products.
18945004
The alpha subunit of the Saccharomyces cerevisiae oligosaccharyltransferase complex is essential for vegetative growth of yeast and is homologous to mammalian ribophorin I
Oligosaccharyltransferase mediates the transfer of a preassembled high mannose oligosaccharide from a lipid-linked oligosaccharide donor to consensus glycosylation acceptor sites in newly synthesized proteins in the lumen of the rough endoplasmic reticulum. The Saccharomyces cerevisiae oligosaccharyltransferase is an oligomeric complex composed of six nonidentical subunits (alpha-zeta), two of which are glycoproteins (alpha and beta). The beta and delta subunits of the oligosaccharyltransferase are encoded by the WBP1 and SWP1 genes. Here we describe the functional characterization of the OST1 gene that encodes the alpha subunit of the oligosaccharyltransferase. Protein sequence analysis revealed a significant sequence identity between the Saccharomyces cerevisiae Ost1 protein and ribophorin I, a previously identified subunit of the mammalian oligosaccharyltransferase. A disruption of the OST1 locus was not tolerated in haploid yeast showing that expression of the Ost1 protein is essential for vegetative growth of yeast. An analysis of a series of conditional ost1 mutants demonstrated that defects in the Ost1 protein cause pleiotropic underglycosylation of soluble and membrane-bound glycoproteins at both the permissive and restrictive growth temperatures. Microsomal membranes isolated from ost1 mutant yeast showed marked reductions in the in vitro transfer of high mannose oligosaccharide from exogenous lipid-linked oligosaccharide to a glycosylation site acceptor tripeptide. Microsomal membranes isolated from the ost1 mutants contained elevated amounts of the Kar2 stress-response protein.
21025745
Sequence differences between glycosylated and non-glycosylated Asn-X-Thr/Ser acceptor sites: implications for protein engineering
Abstract In N-glycosylated glycoproteins, carbohydrate is attached to Asn in the sequence Asn-X-Ser/Thr, where X denotes any amino acid. However, the presence of this consensus peptide does not always lead to glycosylation. We have compiled an extensive collection of glycosylated and non-glycosylated Asn-X-Thr/Ser sites and present a statistical study based on this data set. Our results indicate that non-glycosylated sites tend to be found more frequently towards the C termini of glycoproteins, and that proline residues in positions X and Y in the consensus Asn-X-Thr/Ser-Y strongly reduce the likelihood of N-linked glycosylation. Beyond this, there are no obvious local sequence features that seem to correlate with the absence or presence of N-linked glycosylation. These findings are discussed in terms of the prediction and engineering of glycosylation sites in secretory proteins.
43562267
Intracellular Folding of Tissue-type Plasminogen Activator
The addition of N-linked core oligosaccharides to membrane and secretory glycoproteins occurs co-translationally at asparagine residues in the tripeptide sequon Asn-Xaa-Ser/Thr soon after translocation of the nascent polypeptide into the lumen of the endoplasmic reticulum. However, the presence of the sequon does not automatically ensure core glycosylation, as many proteins contain sequons that remain either unglycosylated or glycosylated to a variable extent. To investigate whether intracellular protein folding can influence sequon utilization, we have expressed tissue-type plasminogen activator (t-PA) in cell culture in the presence of mild concentrations of the reducing agent dithiothreitol to prevent co-translational disulfide bond formation in the endoplasmic reticulum. We show that conditions that prevent disulfide bond formation lead to complete glycosylation of a sequon that otherwise undergoes variable glycosylation in untreated cells. This demonstrated that folding and disulfide bond formation of t-PA determines its extent of core N-linked glycosylation. When dithiothreitol was removed from the cells, the reduced and overglycosylated t-PA formed disulfide bonds, folded, and was secreted. We also show t-PA present within cells is more susceptible to reduction with low concentrations of dithiothreitol than secreted t-PA.
19673950
The role of the individual cysteine residues in the formation of the mature, antigenic HN protein of Newcastle disease virus.
The amino acid sequence of the hemagglutinin-neuraminidase (HN) glycoprotein of Newcastle disease virus (NDV) has 14 cysteine residues, two of which are variably present in the sequences of the HN proteins of different strains of NDV while the rest are absolutely conserved. The role of each residue in the formation of the mature, oligomeric structure of the HN protein was assessed by characterizing proteins with mutations in each of the cysteine residues by Western analysis, immunoprecipitation with conformationally sensitive antibodies, immunofluorescence, and sedimentation on sucrose gradients. Proteins with mutations in the first cysteine (amino acid 6) or the second cysteine (amino acid 123), the nonconserved cysteine residues, formed antigenically mature oligomers which were transported to the cell surface like wild type. Protein with a mutation at cysteine 2 did not, however, form covalently linked oligomers demonstrating that it is this residue that is responsible for intermolecular disulfide bonds in the mature oligomer. Proteins with mutations in cysteine 3 (amino acid 172) or cysteine 5 (amino acid 196) formed proteins with all antigenic sites except one, site 23. These mutant proteins formed disulfide-linked dimers and were efficiently transported to the cell surface. They did not, however, sediment on gradients like the wild-type protein. They were also defective in the biological activities associated with the wild-type protein. Proteins with mutations in cysteines 4 (amino acid 186), 6 (amino acid 238), 7 (amino acid 247), 8 (amino acid 251), 13 (amino acid 531), or 14 (amino acid 542) contained no mature antigenic sites but formed noncovalently linked oligomers. Proteins with mutations in cysteines 9 (amino acid 344), 10 (amino acid 455), 11 (amino acid 461), or 12 (amino acid 465) formed proteins with antigenic site 4 but no other mature antigenic sites. These mutant proteins also formed noncovalently linked oligomers. These results suggest that mutations in different cysteine residues block the maturation of the HN protein at different stages.
11924504
Efficiency of N-linked core glycosylation at asparagine-319 of rabies virus glycoprotein is altered by deletions C-terminal to the glycosylation sequon.
In N-linked core glycosylation, the oligosaccharide Glc3Man9GlcNAc2 is transferred to the tripeptide sequon Asn-X-Ser/Thr. However, this process must be regulated by additional protein signals, since many sequons are either poorly glycosylated or not glycosylated at all. Since N-linked glycosylation can influence protein structure and function, understanding these signals is essential for the design and expression of recombinant glycoproteins. Core glycosylation usually occurs cotranslationally in the rough endoplasmic reticulum (RER) during translocation of nascent proteins. Since only regions of a protein immediately near to a sequon or N-terminal to it are thought to be in the RER when core glycosylation occurs, most models predict that regions C-terminal to the sequon do not influence this process. We tested whether regions C-terminal to a sequon can influence its core glycosylation. Full-length (505 amino acid) rabies virus glycoprotein (RGP) mutants, each containing only one of the three sequons normally present in RGP, were used for these studies. Using a cell-free system, the core glycosylation efficiency at each sequon was determined. Termination codons were then introduced into these mutants at defined sites to produce C-terminal truncations, and the effect of each of these truncations on the core glycosylation efficiency at each sequon was assessed. While deletion of the C-terminal transmembrane and cytoplasmic domains did not affect core glycosylation, more extensive C-terminal deletions did result in altered core glycosylation in a site-specific fashion. Specifically, C-terminal truncations resulting in proteins containing 386 or 344 amino acids decreased the efficiency of core glycosylation at Asn319. This demonstrates that core glycosylation efficiency can be influenced by the presence or absence of regions in a protein more than 68 amino acids C-terminal to a specific glycosylation site.
9591042
Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase.
A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction. The enzyme, isolated from Thermus aquaticus, greatly simplifies the procedure and, by enabling the amplification reaction to be performed at higher temperatures, significantly improves the specificity, yield, sensitivity, and length of products that can be amplified. Single-copy genomic sequences were amplified by a factor of more than 10 million with very high specificity, and DNA segments up to 2000 base pairs were readily amplified. In addition, the method was used to amplify and detect a target DNA molecule present only once in a sample of 10(5) cells.
12981009
Rapid and reliable protocol for direct sequencing of material amplified by the polymerase chain reaction.
A simple and reliable method is described for direct sequencing of material generated by the polymerase chain reaction. The protocol is based on the purification of the amplified double-stranded product by polyethylene glycol precipitation, annealing of primer with template by a "snap-cooling" procedure and sequencing by the dideoxy chain termination method with the use of Klenow fragment or Taq polymerase. The limit of the size of PCR products that can be sequenced is also discussed.
85658872
Molecular Cloning: A Laboratory Manual
Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential. Molecular Cloning, Fourth Edition, by the celebrated founding author Joe Sambrook and new co-author, the distinguished HHMI investigator Michael Green, preserves the highly praised detail and clarity of previous editions and includes specific chapters and protocols commissioned for the book from expert practitioners at Yale, U Mass, Rockefeller University, Texas Tech, Cold Spring Harbor Laboratory, Washington University, and other leading institutions. The theoretical and historical underpinnings of techniques are prominent features of the presentation throughout, information that does much to help trouble-shoot experimental problems. For the fourth edition of this classic work, the content has been entirely recast to include nucleic-acid based methods selected as the most widely used and valuable in molecular and cellular biology laboratories. Core chapters from the third edition have been revised to feature current strategies and approaches to the preparation and cloning of nucleic acids, gene transfer, and expression analysis. They are augmented by 12 new chapters which show how DNA, RNA, and proteins should be prepared, evaluated, and manipulated, and how data generation and analysis can be handled. The new content includes methods for studying interactions between cellular components, such as microarrays, next-generation sequencing technologies, RNA interference, and epigenetic analysis using DNA methylation techniques and chromatin immunoprecipitation. To make sense of the wealth of data produced by these techniques, a bioinformatics chapter describes the use of analytical tools for comparing sequences of genes and proteins and identifying common expression patterns among sets of genes. Building on thirty years of trust, reliability, and authority, the fourth edition of Mol
26460032
DNA sequencing with chain-terminating inhibitors.
A new method for determining nucleotide sequences in DNA is described. It is similar to the "plus and minus" method [Sanger, F. & Coulson, A. R. (1975) J. Mol. Biol. 94, 441-448] but makes use of the 2',3'-dideoxy and arabinonucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase. The technique has been applied to the DNA of bacteriophage varphiX174 and is more rapid and more accurate than either the plus or the minus method.
9565525
A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.
A series of yeast shuttle vectors and host strains has been created to allow more efficient manipulation of DNA in Saccharomyces cerevisiae. Transplacement vectors were constructed and used to derive yeast strains containing nonreverting his3, trp1, leu2 and ura3 mutations. A set of YCp and YIp vectors (pRS series) was then made based on the backbone of the multipurpose plasmid pBLUESCRIPT. These pRS vectors are all uniform in structure and differ only in the yeast selectable marker gene used (HIS3, TRP1, LEU2 and URA3). They possess all of the attributes of pBLUESCRIPT and several yeast-specific features as well. Using a pRS vector, one can perform most standard DNA manipulations in the same plasmid that is introduced into yeast.
37844720
A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli.
A procedure for the rapid isolation of DNA from the yeast Saccharomyces cerevisiae is described. To release plasmid DNA for the transformation of Escherichia coli, cells are subjected to vortex mixing in the presence of acid-washed glass beads, Triton X-100, sodium dodecyl sulfate, phenol and chloroform. Centrifugation of this mixture separates the DNA from cellular debris. E. coli can be efficiently transformed with plasmid present in the aqueous layer without further purification of the plasmid DNA. This procedure also releases chromosomal DNA. Following two ethanol precipitations, the chromosomal DNA can be digested by restriction endonucleases and analysed by Southern blot analysis.
35889280
A hitchhiker's guide to analysis of the secretory pathway in yeast.
Publisher Summary This chapter presents the analysis of the secretory pathway in yeast. The highly compartmentalized organization of cellular activities in the budding yeast, Saccharomyces cerevisiae , requires a mechanism that ensures the correct localization of protein and lipid. All cellular protein biosynthesis operates in the cytoplasm except for a small number of mitochondrial DNA-encoded proteins. Secretory proteins are synthesized on polyribosomes that preferentially associate with the endoplasmic reticulum (ER) shortly after initiation and discharge the nascent polypeptides into the ER. In yeast secretory proteins, the N-linked core oligosaccharides are trimmed to Man 8 GlcNAc 2 and are extensively modified with additional mannose residues during their transit through the Golgi apparatus, producing a carbohydrate structure referred to as the “outer chain.” Protein secretion and plasma membrane assembly in S .cerevisiae are directed topologically to the bud portion of a growing cell, this region being the region of active cell surface growth. For 35 S or 32 P radiolabeling, the appropriate growth conditions depend largely on the proteins to be examined. Expression of a variety of regulated secretory and membrane proteins require growth conditions that starve yeast of a particular catabolite. Two commonly studied yeast proteins—the α -cell-specific mating pheromone ( α -factor) and the soluble vacuolar protease (CPY)—are produced constitutively.
10537301
Morphological classification of the yeast vacuolar protein sorting mutants: evidence for a prevacuolar compartment in class E vps mutants.
The collection of vacuolar protein sorting mutants (vps mutants) in Saccharomyces cerevisiae comprises of 41 complementation groups. The vacuoles in these mutant strains were examined using immunofluorescence microscopy. Most of the vps mutants were found to possess vacuolar morphologies that differed significantly from wild-type vacuoles. Furthermore, mutants representing independent vps complementation groups were found to share aberrant morphological features. Six distinct classes of vacuolar morphology were observed. Mutants from eight vps complementation groups were defective both for vacuolar segregation from mother cells into developing buds and for acidification of the vacuole. Another group of mutants, represented by 13 complementation groups, accumulated a novel organelle distinct from the vacuole that contained a late-Golgi protein, active vacuolar H(+)-ATPase complex, and soluble vacuolar hydrolases. We suggest that this organelle may represent an exaggerated endosome-like compartment. None of the vps mutants appeared to mislocalize significant amounts of the vacuolar membrane protein alkaline phosphatase. Quantitative immunoprecipitations of the soluble vacuolar hydrolase carboxypeptidase Y (CPY) were performed to determine the extent of the sorting defect in each vps mutant. A good correlation between morphological phenotype and the extent of the CPY sorting defect was observed.
45581318
A new method for predicting signal sequence cleavage sites.
A new method for identifying secretory signal sequences and for predicting the site of cleavage between a signal sequence and the mature exported protein is described. The predictive accuracy is estimated to be around 75-80% for both prokaryotic and eukaryotic proteins.
14441902
Basic local alignment search tool.
A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
12610022
Early stages in the yeast secretory pathway are required for transport of carboxypeptidase Y to the vacuole
Temperature-sensitive secretory mutants (sec) of S. cerevisiae have been used to evaluate the organelles and cellular functions involved in transport of the vacuolar glycoprotein, carboxypeptidase Y (CPY). Others have shown that CPY (61 kd) is synthesized as an inactive proenzyme (69 kd) that is matured by cleavage of an 8 kd amino-terminal propeptide. sec mutants that are blocked in either of two early stages in the secretory process and accumulate endoplasmic reticulum or Golgi bodies also accumulate precursor forms of CPY when cells are incubated at the nonpermissive temperature (37 degrees C). These forms are converted to a proper size when cells are returned to a permissive temperature (25 degrees C). Vacuoles isolated from sec mutant cells do not contain the proCPY produced at 37 degrees C. These results suggest that vacuolar and secretory glycoproteins require the same cellular functions for transport from the endoplasmic reticulum and from the Golgi body. The Golgi body represents a branch point in the pathway: from this organelle, vacuolar proenzymes are transported to the vacuole for proteolytic processing and secretory proteins are packaged into vesicles.
12670958
Structure, biosynthesis, and localization of dipeptidyl aminopeptidase B, an integral membrane glycoprotein of the yeast vacuole
We have characterized the structure, biogenesis, and localization of dipeptidyl aminopeptidase B (DPAP B), a membrane protein of the yeast vacuole. An antibody specific for DPAP B recognizes a 120-kD glycoprotein in yeast that behaves like an integral membrane protein in that it is not removed from membranes by high pH Na2CO3 treatment. Inspection of the deduced amino acid sequence of DPAP B reveals a hydrophobic domain near the NH2 terminus that could potentially span a lipid bilayer. The in vitro enzymatic activity and apparent molecular weight of DPAP B are unaffected by the allelic state of PEP4, a gene essential for the proteolytic activation of a number of soluble vacuolar hydrolases. DPAP B is synthesized as a glycosylated precursor that is converted to the mature 120-kD species by carbohydrate addition. The precursor form of DPAP B accumulates in sec mutants (Novick, P., C. Field, and R. Schekman. 1980. Cell. 21:205-215) that are blocked at the ER (sec18) or Golgi apparatus (sec7), but not at secretory vesicles (sec1). Immunolocalization of DPAP B in wild-type or sec1 mutant cells shows that the protein resides in the vacuolar membrane. However, it is present in non-vacuolar compartments in sec18 and sec7 cells, confirming that the delivery of DPAP B is blocked in these mutants. Interestingly, DPAP B appears to stain the nuclear envelope in a sec18 mutant, which is consistent with the accumulation of DPAP B in the ER membrane at the restrictive temperature. These results suggest that soluble and membrane-bound vacuolar proteins use the same stages of the secretory pathway for their transport.
1036657
Yeast mutants deficient in protein glycosylation.
The synthesis of asparagine-linked oligosaccharides involves the formation of a lipid-linked precursor oligosaccharide that has the composition Glc3Man9GlcNAc2. We have used a [3H]mannose suicide selection to obtain mutants in yeast that are blocked in the synthesis of this precursor oligosaccharide. The alg1 mutant accumulated lipid-linked GlcNAc2, alg2 mutants accumulated Man1-2GlcNAc2, alg3 mutants accumulated Man5GlcNAc2, alg4 mutants accumulated Man1-8GlcNAc2, and alg5 and alg6 mutants accumulated Man9GlcNAc2. Some of these mutants appeared to transfer oligosaccharides other than Glc3Man9GlcNAc2 from the lipid carrier to invertase. These aberrant protein-linked oligosaccharides were processed by the addition of outer chain residues in the alg3, alg5, and alg6 mutants. There was virtually no outer chain addition in the alg2 and alg4 mutants. alg4 was the only mutant that failed to secrete invertase.
37952149
New phenotype of mutations deficient in glucosylation of the lipid-linked oligosaccharide: cloning of the ALG8 locus.
Glc3Man9GlcNAc2 is the preferred substrate of the oligosaccharyltransferase of N-linked glycosylation of proteins, but nonglucosylated oligosaccharides can be transferred to proteins in Saccharomyces cerevisiae. Mutations affecting the addition of the three terminal glucose residues lead to accumulation of Man9GlcNAc2 or Glc1Man9GlcNAc2 in vivo but do not show any detectable growth defect. When these mutations were introduced into a strain with reduced oligosaccharyltransferase activity (due to the wbp1-1 mutation), a severe growth defect was observed: accumulation of suboptimal lipid-linked oligosaccharide and reduced oligosaccharyltransferase activity resulted in a severe underglycosylation of secreted proteins. This new synthetic phenotype made it possible to isolate the ALG8 locus, encoding a potential glucosyltransferase of the endoplasmic reticulum. The ALG8 protein is a 63.5-kDa hydrophobic protein that is not essential for the vegetative growth of yeast. However, the lack of this protein resulted in underglycosylation of secreted proteins.
34245528
Effect of glucosylation of lipid intermediates on oligosaccharide transfer in solubilized microsomes from Saccharomyces cerevisiae.
Glc3Man9GlcNAc2-P-P-dolichol and Man9GlcNAc2-P-P-dolichol isolated from Saccharomyces cerevisiae are substrates for the N-glycosylation of endogenous proteins in Triton X-100-solubilized yeast microsomes. The solubilized oligosaccharide transferase requires Mn2+ for activity; neither Mg2+ nor Ca2+ is an effective substitute. The pH optimum of the transfer reaction is between 6.5 and 7.5. Unlike animal systems, which utilize glucosylated oligosaccharide-lipid to a much greater extent than the unglucosylated species as a donor in the transferase rection, yeast extracts transfer more than 70% of Glc3Man9GlcNAc2 and Man9GlcNAc2 from their respective oligosaccharide-lipids to proteins. However, the rate of N-glycosylation in vitro is approximately 25-fold faster with Glc3Man9GlcNAc2-P-P-dolichol than with Man9GlcNAc2-P-P-dolichol. The apparent Km value for the glucosylated species is 75 nM, while that for the unglucosylated glycolipid is 55 nM.
46305457
Compartmentalized assembly of oligosaccharides on exported glycoproteins in yeast
Temperature-sensitive secretory mutants (sec) of S. cerevisiae have been used to evaluate the stages and localization of glycoprotein oligosaccharide synthesis. At the nonpermissive growth temperature (37 degrees C), the sec mutants accumulate secretory organelles and glycoproteins. Histochemical staining and thin-section electron microscopy reveal that the secreted glycoprotein, acid phosphatase, is contained within one of three distinct organelles that accumulates in different mutants: ER; Golgi-like structures called Berkeley bodies; and 80--100 nm vesicles. When produced at 37 degrees C, invertase and acid phosphatase have less carbohydrate in the mutants that accumulate ER than in other mutants, or than in the wild-type strain. External invertase migrates on SDS-polyacrylamide gels as a heterogeneous species with an apparent molecular weight of 100 to 140 kd. Radiolabeled invertase, immunoprecipitated from extracts of ER-accumulating mutant cells, migrates as a set of three discrete protein species with apparent molecular weights of 79, 81, and 83 kd; the other mutants produce a form more like the secreted enzyme. In each case, removal of N-glycosidically linked oligosaccharides by treatment with endoglycosidase H produces a discrete species that migrates as a protein of 61 kd. Immunochemical analysis of bulk glycoprotein accumulated in the mutants suggests that a major portion of the N-linked oligosaccharide, the outer chain, is added after material passes from the ER.
26031601
Characterization of the glycosylation sites in yeast external invertase. I. N-linked oligosaccharide content of the individual sequons.
External invertase is the product of the SUC2 gene of Saccharomyces cerevisiae. The deduced sequence of this enzyme (Taussig, R., and Carlson, M. (1983) Nucleic Acid Res. 11, 1943-1954) reveals it to contain 14 potential N-linked glycosylation sites, or sequons, although only 9-10 appear to be glycosylated (Trimble, R. B., and Maley, F. (1977) J. Biol. Chem. 252, 4409-4412). To determine the location of the glycosylated sequons, external invertase was deglycosylated with endo-beta-acetylglucosaminidase H and its component peptides analyzed by both fast atom bombardment mass spectrometry (FABMS) and classical peptide isolation procedures. By use of the former technique most of the glucosamine-containing sequons could be located and by the latter sufficient amounts of small glucosamine-containing peptides were isolated to enable their quantitation. From the combined FABMS and glucosamine analyses, it was established that eight of the sequons in a subunit of invertase are either completely or almost completely glycosylated, while five others are glycosylated to the extent of about 50% or less. In the case of two overlapping sequons (4 and 5), which include Asn92-Asn93-Thr-Ser, only the first Asn was glycosylated. Thus, all but one of the sequons of external invertase are glycosylated to some extent, giving an appearance of only 9-10 N-linked oligosaccharides/subunit. The sequence identity of both external and internal invertase was verified by FABMS and by peptide sequence analysis. In only one site was an amino acid found to differ from that deduced from the DNA sequence of the SUC2 gene. This occurred at position 390 where a proline was found in place of alanine, which could result from a single base change in the triplet specifying the latter amino acid.
8879377
Guanosine diphosphatase is required for protein and sphingolipid glycosylation in the Golgi lumen of Saccharomyces cerevisiae
Current models for nucleotide sugar use in the Golgi apparatus predict a critical role for the lumenal nucleoside diphosphatase. After transfer of sugars to endogenous macromolecular acceptors, the enzyme converts nucleoside diphosphates to nucleoside monophosphates which in turn exit the Golgi lumen in a coupled antiporter reaction, allowing entry of additional nucleotide sugar from the cytosol. To test this model, we cloned the gene for the S. cerevisiae guanosine diphosphatase and constructed a null mutation. This mutation should reduce the concentrations of GDP-mannose and GMP and increase the concentration of GDP in the Golgi lumen. The alterations should in turn decrease mannosylation of proteins and lipids in this compartment. In fact, we found a partial block in O- and N-glycosylation of proteins such as chitinase and carboxypeptidase Y and underglycosylation of invertase. In addition, mannosylinositolphosphorylceramide levels were drastically reduced.
25254696
Sulfhydryl modification of the yeast Wbp1p inhibits oligosaccharyl transferase activity.
Chemical labeling of the multimeric Saccharomyces cerevisiae oligosaccharyl transferase indicates that the 48 kDa Wbp1p subunit is an integral component of the catalytically active enzyme. The enzyme was purified following chromatography on concanavalin A agarose, heparin agarose, Q-Sepharose, and hydroxyapatite media. The enzyme activity copurified with a tetrameric complex of polypeptide subunits. Two of the subunits have been identified as the yeast proteins Wbp1p and Swp1p by amino-terminal residue sequencing. A third subunit was identified as a variably glycosylated polypeptide near 64 kDa; preliminary amino acid sequencing showed no identity to known yeast proteins. Modification of a cysteine residue by the reagent methyl methanethiolsulfonate (MMTS) caused time-dependent and concentration-dependent inactivation of the enzyme. To identify the modified subunit of the transferase complex, the labeling reagent S-[(N-biotinoylamino)ethyl] methanethiolsulfonate (BMTS) was synthesized. Like MMTS, BMTS inactivated the oligosaccharyl transferase in a time-dependent manner. Additionally, incubation with the substrate (dolichylpyrophosphoryl)-N,N'-diacetylchitobiose [Dol-PP(GlcNAc)2] protected the enzyme from BMTS inactivation. When the purified enzyme complex was incubated with BMTS, Wbp1p alone was specifically labeled, thereby associating this subunit with catalysis and the binding of the dolichylpyrophosphoryl oligosaccharide substrate in the transferase reaction.