bluuebunny/crossref_metadata_2025_split huggingface dataset:
SEC62
Authors: Deshaies R 
Published: November 2023

Abstract
sec62 mutants were originally identified in a selection for conditional lethal mutants that fail to localize a signal peptide-containing His4 chimera to the ER lumen1. Various derivations of this selection scheme have yielded mutant alleles of three other genes: sec611(see p. 31), sec632(see p. 34), and sec653(see p. 28). sec62 mutants accumulate untranslocated precursor forms of several secretory pathway polypeptides, including alpha factor and carboxypeptidase Y. The translocation of some proteins, including invertase, is only weakly affected by the sec62 mutation, whereas others, including dipeptidylaminopeptidase B, are not affected at aII. Whereas sec62 cells are temperaturesensitive for growth, they exhibit severe defects in protein translocation even at the “permissive” temperature of 24°C. Growth at lower temperatures (17°(), however, restores translocation to nearly wild type levels2. Deletion of SEC62 is lethaI4, indicating that it is an essential gene.
SEC63
Authors: Feldheim D A 
Published: November 2023

Abstract
Temperature-sensitive, conditionally-lethal sec63 mutants were identified by a genetic selection for mutant yeast cells that fail to translocate a signal peptide-cytosolic enzyme hybrid protein3 sec63 accumulates in the cytosol the precursor forms of a variety of soluble secretory and vacuolar precursors. Null alleles of SEC63 are inviable at all temperatures, indicating that this gene is essential.
SEC66
Authors: Fcldheim D A 
Published: November 2023

Abstract
Sec66p was identified as a 31.5 kDa glycoprotein that coprecipitated in an immune complex with Sec62p when radiolabeled, detergent solubilized membrane proteins were immunoprecipitated with anti-Sec62p antibodies under non-denaturing conditions2 Subsequently, it was shown that anti-Sec63p antibodies could also co-immune precipitate Sec66p3. Native Sec66p was purified in quantities suitable for microsequencing using large scale immunoprecipitation. HSS1 was isolated as an allelespecific high copy suppressor of sec63-1011 HSS1 was cloned and sequenced and found to be identical to SEC66.
SEC70
Authors: Green N 
Published: November 2023

Abstract
Mutants were isolated based on their inability to insert into the membrane of the ER a membrane-bound fusion protein consisting of the N-terminal 255 residues of arginine permease and the complete histidinol dehydrogenase sequence encoded by the HIS4C region of HIS412Three independent mutants, secl0-2, secl0-3 and secl0-4, inefficiently translocated the histidinol dehydrogenase portion of the fusion protein across the ER membrane. However, these mutant alleles showed little or no inhibition of the translocation of the dehydrogenase when it was placed behind only the N-terminal 189 residues of arginine permease.
SEC53
Authors: és F K ép 
Published: November 2023

Abstract
Temperature-sensitive, conditionally-lethal sec53 mutants were selected on the basis of accumulation of inactive precursors of secreted proteins2. Temperature-sensitive a/g4 mutants were selected by their survival after a prolonged exposure to tritiated mannose. Cells that efficiently incorporated the labeled sugar were killed by self-irradiation. The best characterized sec53 allele, sec53-6, shows the strongest phenotype. At restrictive temperature, sec53-6, like alg4-9, accumulate inactive and incompletely glycosylated forms of secretory proteins within the lumen of the ER.
α,-glucosidase I
Authors: Trimble R , Moremcn, K , Herscovics A 
Published: November 2023

Abstract
Studies on partially1 and fully2 purified a-glucosidase from S. cerevisiae membrane preparations demonstrated that this enzyme removes a single glucose residue from Glc3Man9GlcNAc2. The enzyme, which has a subunit molecular mass of 95 kDa, has a pH optimum of 6.4-6.8 and does not act on aryl a-glucosides.
Docking protein/SRP receptor
Authors: Meyer D I 
Published: November 2023

Abstract
A 60 kDa proteolytic (elastase) fragment of docking protein (DP) originally isolated from canine pancreatic rough microsome was found to be required for protein translocation across ER membranes in cell-free assays12. Antibodies raised against the purified fragment were used to identify the parent molecule, an ER membrane protein with an apparent molecular weight of 72 kDa3 Functional studies revealed that docking protein was able to release the SRPmediated translational arrest in wheat germ lysate4,5 On the basis of this activity, Gilmore and colleagues independently isolated the intact, 72 kDa form from detergent-solubilized membranes by SRP-affinity chromatography.
TRAM
Authors: Hartmann E , Rapoport T A 
Published: November 2023

Abstract
The TRAM protein is an integral glycosylated membrane protein of 373 amino acids having an apparant molecular weight in SDS gels of 36 kDa. It probably spans the phospholipid bilayer eight times and has a (-terminal tail of about 60 residues. It contains one N-linked carbohydrate chain. Highly homologous sequences were obtained by cDNA cloning from MDCK (canine) and from HeLa (human) cells. They are available in the GenBank under the accession numbers X63678 and X63679, respectively1. No homology to any other known sequence in the EMBUGenBank database could be detected. The TRAM protein is present in the rough ER in amounts at least equivalent to that of membrane bound ribosomes.
Signal sequence receptor (SSR) complex
Authors: Hartmann E , Rapoport T A 
Published: November 2023

Abstract
The $SR-complex has been purified from microsomal membranes of dog pancreas as a tetramer containing four polypeptides (SSRa, SSR . SSRy, SSRo) in stoichiometric relation (relative molecular mass 34 kDa, 22 kDa, 20 kDa, 18 kDa, respectively)1·3. Crosslinking with a bifunctional reagent indicates that the tetrameric complex exists in intact membranes. All subunits are integral membrane proteins12A- The a, . and 8-subunits span the membrane once with the (-termini located in the cytoplasm and the N-termini being translocated .
BiP
Authors: Gething M J 
Published: November 2023

Abstract
The nucleotide sequences of BiP cDNAs cloned from mammalian species4·7 (GenBank Accession numbers M19645 and M17169) predict a protein of 635 amino acids that includes an 18 residue N-terminal signal sequence, and a (terminal tetrapeptide (Lys-Asp-Glu-Leu or KDEL) required for retrieval of BiP molecules that leave the ER. Clusters of acidic amino acids, thought to be involved in the low affinity, high capacity ca++ binding activity of the molecule9, are found at both the N- and (-termini of the molecule. BiP proteins are highly conserved, there being 99% amino acid sequence identity between the mature proteins from human and rodent cells7 and 67% identity between the proteins from mouse cells and from the yeast, Saccharomyces cerevisiae10-12 (Kar2p; see p. 41). Comparison of the sequences of BiP proteins with those of other members of the stress-70 family reveal that the Nterminal two-thirds (-450 amino acids) are much more highly conserved than the (-terminal portions, suggesting a conserved domain followed by a more variable region13,14 (Fig. 1A).
Microsomal signal peptidase complex
Authors: Shelness G 
Published: November 2023

Abstract
Signal peptidase activity was first observed in vitro during cell free translation of secretory precursor mRNAs in the presence of canine pancreas rough microsomes. Preproteins expressed in this system are co-translationally translocated into microsomal vesicles and simultaneouslyprocessed to form the mature polypeptides1.
Oligosaccharide-P-P-dolichol assembly
Authors: Krag S S 
Published: November 2023

Abstract
phorylated family of polyisoprenols containing 17 to 21 isoprenyl groups and having the alpha isoprenyl group saturated. The early biosynthetic steps of dolichyl phosphate are identical to those for cholesterol (Figure 1). Acetyl coenzyme A (CoA) is converted to acetoacetyl CoA; one molecule of each is condensed to form 3-hydroxy-3-methylglutaryi (HMG) CoA. In an important regulatory step catalyzed by HMG-CoA reductase, HMG-CoA undergoes an NADPH-dependent reduction to form mevalonate, which is in turn converted in three ATP-requiring steps followed by loss of a carboxyl group to isopentenylpyrophosphate.
OST48
Authors: Gilmore R 
Published: November 2023

Abstract
The amino acid sequence of OST48 was deduced from the nucleotide sequence of a cDNA cloned from a MDCK cell cDNA library {GenBank accession number M98392)1. The OST48 cDNA clone contains an open reading frame of 445 amino acid residues1. The first 31 residues of the protein resemble a typical cleavable signal sequence for initiation of translocation across the ER membrane. The location of a signal peptidase cleavage site between residues 31 and 32 was predicted using the method of von Heijne2, and subseuently confirmed by sequence analysis of the N-terminus of canine OST48.
N-glycan terocessing in the ER
Authors: Trimbe R , Morcrnen, K , Herscovics A 
Published: November 2023

Abstract
N-linked oligosaccharide synthesis begins with the transfer of a precursor oligosaccharide from a dolichol-P-P-linked intermediate to Asn-X-Ser/Thr. This oligosaccharide, Glc3Man9GlcNAc2, in most cells is then trimmed by a-glucosidases and a,-mannosidases, beginning in the ER. Initial studies on the processing of newly synthesized glycoproteins reported the removal of glucose residues prior to mannose trimming reactions3.4.5. Two glucosidase activitieswere subsequently identified6·8 and termed a-glucosidase I, which removes the terminal a,-1,2-linked glucose from Glc3Man9GlcNAc2, and a-glucosidase II, which removes the remaining two a-1,3-linked glucose residues from the precursor.
Introduction
Authors: Balch W E 
Published: November 2023

Abstract
Export of protein from the ER involves the sequential formation (budding), targeting and fusion of carrier vesicles to the cis Golgi network (CGN), the first compartment of the central Golgi apparatus. Considerable progress has been made in identifying components involved using both biochemical and genetic approaches in yeast and mammalian cells123 While this chapter emphasizes properties unique to each protein, it is important to view their function in a more global perspective. The majority, if not all of the proteins studied to date participate in transport in the context of macromolecular protein complexes. Figure 1 illustrates the extent of these interactions as currently determined from both biochemical and genetic studies. As is readily apparent, interactions are extensive and may occur during synthesis, recycling or the differential steps involved in carrier vesicle budding, targeting and fusion.
SEC16
Authors: Kaiser B 
Published: November 2023

Abstract
The SEC16 gene was first identified in a screen for conditional mutants that block secretory protein transport to the cell surface. At the nonpermissive temperature, sect 6 mutations rapidly cause the accumulation of secretory protein precursors in their core-glycosylated, ER forms, implying a defect in protein transport from the ER. Moreover, by thin-section electron microscopy, sec16 mutants accumulate excess ER membrane at the nonpermissive temperature. More detailed morphological analysis shows that sec16 is in a class of ER-blocked mutants that fail to form a 50 nm vesicle intermediate in transport to the Golgi; in double-mutant epistasis tests, sec16 mutants block the vesicle accumulation that would otherwise occur in sec17, sec18, or sec22 mutants 2 (see pp. 133, 132 and 129).
SEC13
Authors: Pryer N K 
Published: November 2023

Abstract
Two temperature-sensitive alleles, sec13-1 and sec13-4, were isolated by a density enrichment screen1 After a shift to restrictive temperature, sec13-1 cells accumulated exaggerated ER membrane, apparent in thin-section elec tron micrographs2 Mutant cells shifted to the restrictive temperature exhibited a rapid block in secretion of secreted, plasma membrane and vacuolar proteins such as invertase, alkaline phosphatase and carboxypeptidase Y. The blocked proteins accumulated in the core-glycosylated ER form13. A third allele, sec13-5, has recently been isolated in a mutant screen for cells secreting unprocessed a factor4.
YPT1
Authors: Segev N 
Published: November 2023

Abstract
Analysis of the phenotype of several ypt1 mutants indicates that the Ypt1 protein plays an essential role in the secretory pathway3. First, null mutations, generated by gene disruption techniques, reveal that the YPT1 gene is essential for vegetative growth in yeast45. Second, analysis of conditional-lethal mutations suggests that the Ypt1 protein is involved in an early step of protein transport.
SLY1
Authors: Daschcr C , Schmitt H D 
Published: November 2023

Abstract
The null mutation of SLY1 is lethal1 A galactose-dependent conditional lethal mutant with SLY1 under transcriptional control of the regulatable GAL10 promoter grows normally on galactose but ceases growth in glucose-con-taining medium. Under restrictive conditions these mutant cells show a block in protein transport from the ER to the Golgi apparatus: Sly1p-deleted cells accumulate intracellular core-glycosylated invertase and carboxypeptidase Y as well as an excess of ER membranes2.
SEC17d
Authors: Kaiser ¾ C 
Published: November 2023

Abstract
The SEC17 gene was first identified in a screen for conditional mutants that block secretory protein transport to the cell surface. At the nonpermissive temperature, sec17 mutations rapidly cause the accumulation of secretory protein precursors in their core glycosylated, ER forms implying a defect in protein transport from the ER. By thin-section electron microscopy, sec17 mutants accumulate excess ER membrane at the nonpermissive temperature. More detailed morphological analysis shows that sec17 is in a class of ER-blocked mutants that accumulate 50 nm vesicles and are therefore defective in vesicle fusion with the Golgi.
SEC19
Authors: Pryer N K 
Published: November 2023

Abstract
A single temperature-sensitive allele, sec19-1, was isolated by a density enrichment screen. After shifting to restric-tive temperature, mutant cells accumulate a mixture of secretory organelles, including ER membrane, 80-100 nm vesicles (similar in size to mature secretory vesicles), and “Berkeley bodies”, structures thought to represent the Golgi apparatus. The sec19-1 mutant accumulates the p1 (core-glycosylated) form of the vacuolar protease carboxypeptidase Y at the restrictive temperature2 , indicating that the secretory block is imposed on transport between the ER and Golgi.
SED5
Authors: Pelham H 
Published: November 2023

Abstract
Deletion of the SED5 gene is lethal. When cells are depleted of Sed5 protein by repression of a GAL promoterSEDS fusion gene, transport of proteins from the ER to the Golgi is blocked and there is an accumulation of ER membranes and small vesicles1 The DNA sequence of the SED5 gene (GenBank accession number X66980) predicts a protein of 340 amino acids (39 kDa).
Coatomer
Authors: Waters M G , Beckers C J M 
Published: November 2023

Abstract
Coatomer was originally purified from bovine brain 1 but has also been purified from bovine liver9 with a higher yield. The original brain protocol employed precipitation of the complex with a low ionic strength acidic (pH 5.8) buffer. Although this precipitation greatly enriches the coatomer, it modifies the coatomer such that it is no longer soluble in physiological salt and must be maintained in high salt buffers. To avoid this difficulty, coatomer has been purified from bovine liver (where it is more abundant) without the precipitation step. This preparation is soluble in physiological salt.
Genes required for the maturation of N-linked carbohydrates in mammalian cells
Authors: Stanley P 
Published: November 2023

Abstract
N-linked glycosylation reactions that begin with the action of GlcNAc-TI are summarized in Figure 1; further information is provided in Table 1. Building of hybrid and complex oligosaccharides proceeds by the action of specific glycosyltransferases that catalyze the transfer of each sugar residue from a nucleotide-sugar to the carbohydrate acceptor in a specific glycosidic linkage. Nucleotide-sugars are synthesized for the most part in the cytoplasm and must be translocated via specific transporters into the Golgi lumen2 The N-linked structures of a glycoprotein exhibit a restricted heterogeneity dependent on several factors, including the protein conformation surrounding the glycosylation site.
Furin
Authors: Thomas F 
Published: November 2023

Abstract
Furin is the translation product encoded by the fur locus, which was initially identified by its proximity to the fes/fps proto-oncogene (fes/fps JJ.pstream region)3. Furin cDNAs have been isolated from several species including human, mouse, rat and Xenopus4-8. Cloning of cDNAs by PCR strategy shows that furin was the first identified member of a growing family of mammalian subtilisin-related K£X2-like endoproteases (designated KLIP’s in reference 9) that currently includes PACE-4, PC2 and PC3 (also called PC1), and PC410-17 (see PC entry p. 197).
PC2 and PC3
Authors: Smeckens S 
Published: November 2023

Abstract
The domain structures of PC2 and PC3 are shown in Figure1. Each protein begins with a signal peptide indicating entry into the secretory pathway, followed by about a 100 residue pro-domain. In the bacterial subtilisins the pro-domain plays a role in protease folding and its removal is necessary for enzyme activation6.7. In the eukaryotic proteases, prodomain cleavage occurs at a conserved motif of basic amino acids, reflecting the substrate specificity of these proteases and suggesting that this cleavage is autocatalytic. Studies indicate that cleavage of the PC3 pro-domain occurs at an early stage during biosynthesis, perhaps in the endoplasmic reticulum.
Synaptobrevin protein family
Authors: Jahn R , Südhof T C 
Published: November 2023

Abstract
In mammalian species, two different synaptobrevin cDNAs have been characterized so far1,2A (GenBank accession numbers VAMP-1: M24105 and VAMP-2: M24104}. They encode two highly homologous proteins, synaptobrevin 1 (VAMP-1} and synaptobrevin 2 (VAMP-2) predicted to contain 118 and 116 amino acid residues, respectively. No evidence for a signal sequence was found. The two forms share 77% amino acid sequence identity. Comparison of the rat and human sequence revealed that each form is separately conserved, with only one and three amino acid substitutions in synaptobrevin 2 and synaptobrevin 1, respectively4. In addition, cDNA sequences of synaptobrevin homologues from Torpedo and Drosophila were reported23
SSA Hsp70 subfamily
Authors: Nelson R J , Craig E 
Published: November 2023

Abstract
The four SSA genes are regulated differently in response to stress and growth state. SSA1 is constitutively expressed as well as being stress-inducible, while SSA2 is constitutive and not ostensibly affected by stress. SSA3 and SSA4 are “classic” heat shock genes whose expression is stress dependent. Also, unlike any other SSA gene, SSA3 transcription is derepressed in response to nutrient limitation2·3.
VPS1
Authors: Raymond C K , Stevens T H 
Published: November 2023

Abstract
The overall identity between Vps1 protein and dynamin (and/or shibire, since dynamin and shibire are ∼90% identi-caI5) is 45%; however, the amino-terminal 300 residues of these proteins share 66% identity4·5. The level of similarity of Vps1 protein to the Mx proteins is -45% over the N-terminal 250 residues, and ∼30% overall1.
VPS16
Authors: Horazdosky B F , Emr S D 
Published: November 2023

Abstract
Cells carrying a complete deletion of the VPS16 coding region are viable, but display a temperature-sensitive growth phenotype1. vps16A cells also exhibit a severe vacuole protein localization defect (secreting &gt;95% of the soluble vacuolar hydrolase, carboxypeptidase Y in its Golgi modified precursor form) and are completely defective in the proteolytic maturation of all vacuolar proteins examined1. In addition, cells carrying the vps16 null allele lack any identifiable vacuolar structure, but instead accumulate small vesicle-like structures typical of class C vps mutants45.
VPS21
Authors: Horazdovsky C F , Busch, G R , Emr S D 
Published: November 2023

Abstract
The loss of Vps21p function severely compromises the ability of yeast cells to localize both soluble and membrane associated vacuolar proteins1. Greater than 80% of two soluble hydrolases, carboxypeptidase Y (CPY) and proteinase A (PrA), are missorted in t,vps21 cells and are present as Golgi modified precursors. A small amount of mature CPY and PrA (∼15% of total) can be detected in the mutant cells.
VPS45
Authors: Piper R C , Stevens T H 
Published: November 2023

Abstract
Haploid cells carrying a 70% deletion of the VPS45 open reading frame (vps45A) are viable but exhibit defective growth at 37°C as observed with many other VPS mutants. vps45A cells secrete &gt;70% of newly synthesized CPY precursors well as other vacuolar hydrolase precursors. vps45A mutants are morphologically distinguished by having large central vacuoles. Newly formed vps45A daughter cells lack vacuolar structures as determined by immunofluorescence with antibodies specific for the vacuolar membrane alkaline phosphatase or the vacuolar H+ATPase. This morphological phenotype results from a defect in vacuolar segregation from mother cells into the developing bud region (see VPS3 entry, p.231).
PEPS
Authors: Woolford C A , Jones E W 
Published: November 2023

Abstract
Haploid cells possessing a deletion/disruption allele of PEPS are viable. peps mutants show greatly decreased activities of the vacuolar hydrolases proteinase A (PrA), proteinase B (PrB), carboxypeptidase Y (CPY) and the repressible alkaline phosphatase2 Normal precursor forms of the proteases accumulate, as do novel forms of PrB antigen. It has been shown that in peps mutants a precursor to CPY78 and precursor and mature forms of PrA78 are mislocalized and secreted. Alpha-factor is internalized, but is not degraded4. Mutants show a growth defect on nonfermentable carbon sources4 A peps null mutant shows very slow growth at 37°C, implying that the PEPS gene product helps in extending the temperature growth range. The vacuolar morphology of peps mutants is quite aberrant.
PEP12
Authors: Bachhawat K A , Jones F W 
Published: November 2023

Abstract
Cells with mutations in the PEP12 gene have one unusually large vacuole. Analysis of insertion/disruption and dele-tion/disruption mutant strains has revealed that the gene product is non-essential invegetatively growing cells. The cell density of the disruption strains at stationary phase however is only -50% of wild type. Cells grown under stressful conditions, however, demonstrate growth difficulties. For example: with glucose as a carbon source, cell doubling time of a strain containing the disruption is only slightly slower than wild type at 30°C. However, at 37°C the growth is greatly slowed. Diploid strains heterozygous for the disruption allele sporulate normally while those homozygous for the disruption allele fail to sporulate.
SRP101
Authors: Ogg S C , Walter P 
Published: November 2023

Abstract
Although SRP101 is not an essential gene, disruption of SRP101 results in an approximate six fold reduction in the growth rate of the cells. In addition, cells which are deleted for SRP101 are unable to grow on carbon sources requiring respiration1 Yeast cells that contain the SRu gene (SRP101) under the control of the GALI promoter show impaired translocation of soluble and membrane proteins across the ER membrane after depletion of SRu1. The degree of this translocation defect varies for different proteins. Kar2p, a soluble ER resident protein, and dipeptidyl aminopeptidase-B (DPAP-B), a vacuolar integral membrane protein, showed the greatest defect.