bluuebunny/crossref_metadata_2025_split huggingface dataset:
SPC21
Authors: Shclncss G 
Published: November 2023

Abstract
The nucleotide sequence of cDNAs encoding SPC 21 (GenBank accession number JO5069}2 predicts a 192 amino acid protein and a calculated molecular mass of 21,585 Da. The sequence is 81% identical to that of SPC 18 (seep. 91) over a 176 residue region of overlap and 47% identical over a 167 residue region of overlap to yeast Sec11 protein (seep. 40). SPC 21 is synthesized without a cleavable amino terminal signal peptide, however, the initiating methionine is removed from the primary translation product2. Recent sequence comparisons among SPC 21, SPC 18, Sec11p, mitochondrial inner membrane protease 1 and several prokaryotic leader peptidases have revealed the presence of several 5-18 amino acid conserved sequence domains3
Ribophorin I and II
Authors: Kreibich G 
Published: November 2023

Abstract
A comparison of SDS polyacrylamide gels of rough and smooth rat liver microsomes first revealed the existence of compositional differences between the continuous membrane system of the rough and smooth endoplasmic reticulum (ER)1·2. Purified rough microsomes (RM) were found to contain two transmembrane glycoproteins3 that are not found in smooth microsomes (SM).
α-Glucosidase I
Authors: Trimble R , Morcmen, K , Herscovics A 
Published: November 2023

Abstract
Initial studies on partially purified a-glucosidase I from rat liver1·2 and oviduct microsomes3 .4 demonstrated that this enzyme removes a single glucose residue from Glc3Man9GlcNAc2. a-Glucosidase I was subsequently purified from calf5 and porcine6 liver, lactating bovine mammary tissue7, mung bean seedlings8, and 5. cerevisiae 9 (see entry, p. 60). It has a pH optimum of 6.4-6.8 and does not act on aryl a-glucosides.
SAR1
Authors: Nakano A 
Published: November 2023

Abstract
The null mutation of SAR1 is lethal. A galactosedependent conditional-lethal mutant has been constructed by placing the SAR1 gene under the control of the GAL1 promoter1. This strain grows normally on galactose medium but ceases growth upon shift to glucose. Under this restrictive condition, the cells accumulate ER-located precursors of a-factor and carboxypeptidase Y.
SEC23
Authors: Hicke L , Schekman R 
Published: November 2023

Abstract
The temperature-sensitive sec23-1 mutant was isolated by density enrichment of nitrous acid-mutagenized yeast cells3 Upon a shift to the nonpermissive temperature (30°(-37°(), sec23 cells very rapidly accumulate core-glycosylated forms of a variety of secretory proteins, a hallmark of defective transport out of the ER3 In addition, electron micrographs demonstrate that the mutant proliferates ER membrane at 37°( but does not accumulate the 50 nm vesicles thought to be transport intermediates between the ER and the Golgi.
SEC24
Authors: oshihisa T Y 
Published: November 2023

Abstract
Sec24p was originally identified as an additional component of the 300 kDa complex containing Sec23p. Antibodies against Sec23p immunoprecipitate Sec24p and biochemical purification of functional Sec23p complex results in the copurification of Sec24p12. Anti-Sec24p antibodies, both affinity purified lgG or Fab fragments, strongly inhibit in vitro vesicle transport between the ER and the Golgi and the formation of ER-derived transport vesicles in semi-intact cells1. These same Sec24p antibodies do not affect the Sar1p-specific GAP activity of the Sec23p/Sec24p complex.
SEC21
Authors: Hosolmchi M 
Published: November 2023

Abstract
A temperature-sensitive mutant, sec21-1, isolated by density enrichment, blocks secretion of invertase and other secretory proteins when shifted to the nonpermissive temperature1. Pulse-chase experiments using labelled carboxypeptidase Y as a marker indicate that accumulated secretory precursors are of the core glycosylated, ER form2 At the non-permissive temperature, sec21-1 cells accumulate ER structures and 50nm vesicles34.
BOS1
Authors: Ferro-Novick S 
Published: November 2023

Abstract
8051 is an essential gene identified by its ability to suppress bet112(see p. 127), a temperature-sensitive mutant that blocks transport from the ER to the Golgi complex3 8051 also suppresses sec222A (see p. 129), but not mutants blocked at other stages of the secretory pathway. The ability of 8051 to specifically suppress two mutants blocked in ER to Golgi transport implies that its product functions in this process. In order to test this hypothesis, we constructed a strain in which the sole copy of 8051 was placed under the control of a regulatable GAL1 promoter. In growth medium containing glucose, the synthesis of Bos1 is repressed in this strain. As a consequence, cells fail to secrete pro-a-factor and to transport carboxypeptidase Y (CPY) to the vacuole. The extent of precursor processing of accumulated pro-a-factor and pro-CPY is consistent with a block in ER to Golgi transport.
BET2
Authors: Ferro-Novick S 
Published: November 2023

Abstract
ORF2, an essential yeast gene of unknown function. The DNA sequences of BET2 and ORF2 are identical with the exception of one nucleotide alteration that results in a conserved amino acid change in the protein (asparagine in Orf2 and lysine in Bet2 at position 22)213. This change may be attributable to differences in strain backgrounds.
ERD2
Authors: Pelham I 
Published: November 2023

Abstract
erd2 mutants were isolated in a screen for cells that secrete proteins bearing the HDEL signal. The mutant cells show no recognition of HDEL, have no detectable defects in other protein sorting pathways and have wild-type growth rates under all conditions tested. However, the ERD2 gene is essential for growth. Depletion of Erd2p in cells leads to an accumulation of internal membranes and to a defect in the transport of proteins through the Golgi apparatus2 This may be due to a requirement for Erd2p in a forward transport step through the Golgi, or an indirect effect of the failure to recycle material from the Golgi back to the ER.
SED4
Authors: Pelham H 
Published: November 2023

Abstract
The SED4 gene is included in the complete sequence of chromosome Ill (GenBank accession number X59720}, and corresponds to the open reading frame designated YCR67c2 The sequence predicts a protein of 1065 amino acids. It has a single predicted transmembrane sequence, and by analogy with Sec12p (see p. 113) is likely to have its N terminus in the cytoplasm. The cytoplasmic domain is 45% identical to that of Sec12p; the luminal domain of Sed4p is considerably larger than that of Sec12p, and does not show significant homology to it.
p63
Authors: Hauri H -P 
Published: November 2023

Abstract
The nucleotide sequence of p63 cDNA (EMBL accession number X69910) cloned from a human placenta cDNA library3 predicts a type II transmembrane protein of 601 amino acid residues without an N-terminal signal sequence. p63 is comprised of a 106 amino acids (N-terminal) cytosolic, a 21 amino acid putative transmembrane sequence, and a large luminal domain. The p63 cDNA sequence lacks consensus sites for N-glycosylation. The cytosolic domain of p63 includes unusual stretches rich in proline, glycine or alanine. The p63 cDNA shows homologies with a pig gene whose expression in the liver is enhanced after resuscitation from circulatory shock4. Hence, p63 may be a stress protein.
Mannosidases of the Golgi complex
Authors: Trimble R B , Morcmcn K , Hcrscovics A 
Published: November 2023

Abstract
The trimming phase of the N-glycan processing pathway is initiated by a-glucosidases I and II and a collection of processing mannosidases in the ER and Golgi complex, which remove the four a1,2-mannose residues to yield Man5GlcNAc2. Following the action of GlcNAc transferase I, which initiates branching of complex oligosaccharides, Golgi a-mannosidase II removes one a1,3- and one a1,6- linked mannose residue to yield GlcNAcMan3GlcNAc2. This structure serves as the substrate for further elaboration of the oligosaccharide chain by the addition of fucose, galactose, and sialic acid residues1 (see entry, p. 190).
Golgi a-mannosidase I
Authors: Trimble R , Moremen, K , Herscovics A 
Published: November 2023

Abstract
a-Mannosidase I was the first Golgi processing a-mannosidase identified in mammalian cells12. The catalytic properties of this enzyme are very similar to those of the ER-located, Ca2+-dependent a1,2-mannosidases described earlier (see entry p. 103). However, a requirement for Ca2+ was not demonstrated, but the effect of Ca2+ was not tested in the presence of EDTA as was done for the other enzymes. The a-mannosidase I activity was resolved further, yielding two components, termed IA and IB, with different chromatographic properties upon ion-exchange chromatography and gel filtration23. Golgi mannosidase IA was purified to homogeneity3 and shown to be a glycoprotein tetramer consisting of 57-58 kDa subunits. The two enzymes have similar oligosaccharide substrate specificities, are both inhibited by 1-deoxymannojirimycin (dMNJ), and share antigenic determinants.
Golgi a-mannosidase II
Authors: Trimble R , Morcmen, K , Herscovics A 
Published: November 2023

Abstract
a-Mannosidase II was originally detected in rat liver Golgi membrane fractions, using p-nitrophenyl-a-D-mannoside as substrate1, as an activity distinct from the lysosomal and soluble a-mannosidases2. The enzyme was subsequently shown to have an extremely restricted specificity toward natural oligosaccharide substrates, removing only the terminal a1,3- and a1,6-linked mannose residues from GlcNAcMan5GlcNAc2 to yield GlcNAcMan3GlcNAc/.
Golgi endo- α-mannosidase
Authors: Spiro R G 
Published: November 2023

Abstract
Endo-a-mannosidase is the only processing enzyme that has been described which trims N-linked oligosaccharides by the removal of more than one sugar residue at a time. Indeed, the discovery of this Golgi enzyme, which specifically cleaves the a.1-2 linkage between the glucose-substituted mannose and the more internal portion of the polymannose unit, has complicated the originally proposed processing scheme by providing an alternate route for achieving glucose removal12.
TGN38/41
Authors: Banting G , Reave B , Wilde A , Luzio J P , Stanley K , Crosby, J , Howell K 
Published: November 2023

Abstract
cDNA clones encoding both TGN38 and TGN41 have been isolated and sequenced (these sequences are present in the GenEMBL database with accession numbers X53565 and X64600). The only difference between the two sequences is a stretch of eight base pairs in the TGN41 sequence which contains a five base pair insertion not found in the TGN38 sequence. This insertion is in the region of the cDNA encoding the cytoplasmic domain of the protein, and leads to a shift in reading frame such that the (-termi-nal cytoplasmic domain of TGN41 is 20 amino acids longer than that of TGN38. The conceptual translation of the TGN38 cDNA sequence predicts a protein with a molecular weight of 38 kDa, that of TGN41 predicts a protein with a molecular weight of 41 kDa.
Rab proteins on the exocytic and endocytic pathway
Authors: Zerial M , Chavrier P , Huber L A , Vingron M , Simons K 
Published: November 2023

Abstract
Mammalian cells express four different sub-families of low molecular weight GTP-binding proteins: RAS/RAP, RAB, RHO and SAR/ARF (see Bourne et al.3 for a review). Rab proteins are the most closely related to the yeast proteins Ypt1p4 (seep. 121) and Sec4p5 (seep. 168). All rab proteins display the four highly conserved regions that participate in the formation of a single GTP-binding site1
Synaptotagmin protein family
Authors: Jahn R , Südhof T C 
Published: November 2023

Abstract
The synaptotagmin protein family so far comprises two members in mammals (synaptotagmin I, GenBank accession number X52772, and synaptotagmin II, GenBank accession number M64499)12 and three members in the electric ray Discopyge ommata3 (GenBank accession numbers M64275, M64276, and M64277). In addition, a synaptotagmin cDNA was cloned from Drosophila4 (GenBank accession number M55048). The rat cDNA for synaptotagmin I encodes a protein predicted to contain 421 amino acid residues1. The protein has no signal sequences and one predicted transmembrane region1, with the N-terminus facing the vesicular lumen.
Introduction
Authors: Stevens T H 
Published: November 2023

Abstract
This section of the Guidebook will focus on the proteins involved in membrane traffic to the eukaryotic lysosome (called the vacuole in yeast cells). The two major pathways to the lysosome/vacuole are the endocytic pathway from the plasma membrane and the biosynthetic pathway from the Golgi complex1 As depicted in Figure 1, these pathways converge at a late-endosomal/prelysosomal compartment. The terminal organelle along each of these pathways is the lysosome, which is an acidic, hydrolase-rich compartment for degradation of macromolecules.
SRP54
Authors: Hann C C , Walter P 
Published: November 2023

Abstract
Gene disruption of 5RP545 Pis a lethal event4 Disruption of 5RP545 cis not lethal but results in slow cell growth (approximately four times slower than wild-type) and a rho-phenotype2. Cells containing the 5RP545 cgene disruption are defective in translocation of precursor proteins. The degree of translocation defect, however, varies for different precursor proteins2. Similar effects are observed during in vivo depletion of the SRP54sc protein.
SEC61
Authors: Stirling D J 
Published: November 2023

Abstract
Temperature sensitive sec61 mutants have been isolated using two related selection procedures. Both selections depend upon the retention of a signal sequence-containing fusion protein within the cytoplasmic compartment. In the first instance, the signal sequence was that of the secretory protein, prepro-a-factor1, whereas the second selection employed the signal sequence of an integral membrane protein, namely hydroxymethylglutarylcoenzyme A reductase.
RalsA
Authors: Chardin Pierre 
Published: November 2023

Abstract
RalA was originally isolated from a simian B-lymphocyte cDNA library (Chardin and Tavitian 1986) (GenBank accession number X04328) and later from a human pheochromocytoma cDNA library (Chardin and Tavitian 1989) (GenBank accession number X15014). The same screening enabled isolation of a second closely related human cDNA: RalB. A partial human RalA cDNA was also cloned from a differentiated HL-60 library, and full length cDNAs were isolated from a placental library (Polakis et al. 1989) (GenBank accession number M29893).
Rapla and Raplb
Authors: Pizon Veronique 
Published: November 2023

Abstract
Two approaches led to the Rapla identification. Rapla was isolated from a Raji human Burkitt lymphoma cDNA library (Pizon et al. 1988a) using the complete insert of the Drosophila Dras3 cDNA as a probe (Schejter and Shilo 1985) and as a phenotypic suppressor of Ras transforming activity (Kitayama etal. 1989). Rapla is also named Krevl. Raplb was identified by screening a human pheochromocytoma cDNA library with the Rapla cDNA (Pizon etal. 1988b). The DNA sequences of the human Rapla and Rap1 b are shown in Fig. 1. GenBank accession numbers for Rapla and Raplb are X12383 and X08004, respectively.
Dictyostelium ras genes
Authors: Daniel Juliet , Weeks Gerald , Spiegelman George B 
Published: November 2023

Abstract
Five ras genes (rasB, rasC, rasD, rasG and rasS) and one rap gene (rap1) have been isolated and characterized in the cellular slime mold Dictyostelium discoideum (Daniel etal. 1993,1994; Reymond etal. 1984; Robbins eta/. 1989,1990). These ras subfamily genes encode 21-22 kDa GTP-binding proteins that have 52-68% amino acid identity with the human H-Ras protein (Table 1). These genes all appear to be present in a single copy since each of their cognate cDNAs hybridizes to a single, unique genomic fragment under high stringency conditions.
Drk
Authors: Olivier J Paul , Pawson Tony 
Published: November 2023

Abstract
Drk was identified by screening a cDNA expression library made from Drosophila embryos at 10-12 h of development using the CORT (Cloning of receptor targets) method (Skolnik et al. 1991;Margolis et al. 1992). The tyrosine phosphorylated C-terminal tail of the activated human EGF receptor, which binds several SH2 domains of mammalian signaling proteins, was used as the probe to identify cDNAs that encode SH2 domains in Drosophila. The DNA sequence of drk (Olivier etal. 1993; Simon eta/. 1993) is shown in Fig. 1. The GenBank accession number is M35520.
GRB2
Authors: Downward Julian 
Published: November 2023

Abstract
it was identified genetically by its involvement in the vulval development pathway (Clark et al. 1992). Human GRB2 cDNA was cloned independently by using the tyrosine phosphorylated C-terminal tail of the EGF receptor to probe a brain XGT11 protein expression library (Lowenstein et al. 1992). The name, standing for growth factor receptor-bound protein 2, reflects the cloning protocol. The rat homologue of GRB2 was cloned independently using a consensus probe for SH2 sequences and was initially named ASH, for abundant Src homology protein (Matuoka et al. 1992).
Neurofibromin
Authors: McCormick Frank 
Published: November 2023

Abstract
ProteinNeurofibromin is a protein of 2818 amino acids with several splicing variants {Gutmann and Collins 1993). The best characterized consists of an extra 21 amino acids inserted in the GTPase-activating protein {GAP)-related domain {Anderson et al. 1993; Mochizuki et al. 1992; Uchida et al. 1992). Differential expression of this form{type II) has been implicated in brain tumors {Suzuki et al. 1991). Neurofibromin is homologous to the yeast IRA genes in regions that extend beyond the GAP-related domain, suggesting that these proteins share additional functions yet to be determined.Posttranslational modificationsNo data is available.
Raf1
Authors: Wood Kenneth W 
Published: November 2023

Abstract
The human cDNA encoding Rafi was originally identified as a cellular homologue of v-raf the transforming gene of murine sarcoma virus 3611. Rafi is the most widely expressed of the raf family of kinases (Storm et al. 1990). The nucleotide and deduced amino acid sequence of human Rafi is shown in Fig. 1.
p62
Authors: McCormick Frank 
Published: November 2023

Abstract
The amino-terminal half of p62 contains a domain with predicted RNA binding properties (Wong etal. 1992). This domain is highly related to a domain found in the Artemia hnRNP protein GRP33. In the C-terminal domain, a region containing 12 arginine-glycine pairs was identified: this is a characteristic of other RNA binding proteins. The site of p120-GAP binding, and of major tyrosine phosphorylation, is at the C-terminus, along with a proline-rich domain, suggesting possible src homology region 3 (SH3) interactions.
Ste6
Authors: Hughes David A , Yamamoto Masayuki 
Published: November 2023

Abstract
The ste6 gene was cloned by functional complementation of the mating defect of a sterile ste6 mutant strain (Hughes et al. 1990). The DNA sequence of a genomic fragment containing the ste6 gene is shown in Fig. 1. From inspection of the DNA sequence there do not appear to be any introns within the gene although this has not been examined experimentally by cDNA cloning. The GenBank accession number is X53254.
RhoD
Authors: Parton Robert G , Zerial Marino 
Published: November 2023

Abstract
RhoD was identified from mouse kidney using a PCR-based approach (Chavrier etal. 1992), and cDNA clones encoding RhoD were obtained (Grummt etal. 1992) using modified RACE protocols on mouse kidney RNA (Frohman et al. 1988). The GenBank accession number is X84325.
pl90
Authors: Settleman Jeffrey 
Published: November 2023

Abstract
The p190 protein was first identified in 1990 as a phosphotyrosine-containing protein that co-immunoprecipitates with p120 Ras-GAP in growth factor-stimulated and tyrosine kinase-transformed cells (Ellis etal. 1990; Moran etal. 1991). Since that time, p190 has not been reported to associate stably with any other proteins or cellular components. p190 does, however, make contact with members of the Rho family of small GTPases, and probably binds directly to guanine nucleotides, as is described in the ‘functional studies’ section.
Rab2
Authors: Balch William E 
Published: November 2023

Abstract
Rab2 was identified by the screening of cDNA libraries from rat, human and canine sources using oligonucleotide probes specific to Ras-related proteins (Touchot et al. 1987; Zahraoui et al. 1989; Chavrier et al. 1990a; Tachibana etal. 1992). The nucleotide sequence of the rat Rab2 is shown in Fig. 1. The GenBank accession number is J02999.
Rab3d
Authors: Scherer Philipp E , Baldini Giulia , F.Lodish Harvey 
Published: November 2023

Abstract
Rab3d was identified by a polymerase chain reaction (PCR)- based approach with degenerate oligonucleotides. Primers encoding the conserved G-3 and G-4 regions in Rab and Ras proteins corresponding to WDTAGQE and GNKXD were designed and a mouse adipocyte-specific subtractive library was used as a template. The PCR products were in turn used to screen the subtractive library (Baldini et al. 1992). This screen yielded two identical clones that hybridized to a message that was induced during adipocyte differentiation. Sequencing revealed an insert encoding a protein with high homology to the Rab3 family and was termed Rab3d. The GenBank accession number is M89777.
Rab4b
Authors: Bucci Cecilia , Zerial Marino 
Published: November 2023

Abstract
Rab4b was identified by Chavrier etal. (1990), screening an MDCKII cell cDNA library with an oligonucleotide corresponding to the amino acid sequence WDTAGQE, which is shared by members of the Rab and Rho protein subfamilies (Valencia 1991). The nucleotide sequence and the predicted amino acid sequence are shown in Fig. 1(A). Northern blot analysis revealed a single ∼2 kb messenger RNA that was expressed in BHK21, MDCKII and NIH3T3 cell lines. The GenBank accession number is X56389.
Rab9
Authors: Pfeffer Suzanne R 
Published: November 2023

Abstract
Rab9 was first identified in a screen for Ypt1 and Sec4 protein-related cDNA clones (Chavrier et al. 1990). The DNA sequence of canine Rab9 (Chavrier et al. 1990; Lombardi et al. 1993) is shown in Figure 1. The GenBank accession number isX56386; Swiss-Prot, P24408.
Rab 10
Authors: Huber Lukas A 
Published: November 2023

Abstract
Rabi 0 was one of the proteins (together with Rab8) identified in the first round of screening of a Madin-Darby canine kidney (MDCK) cDNA library (Zahraoui et al. 1989; Chavrier et al. 1990) with degenerated oligonucleotides corresponding to the amino acid sequence WDTAGQE. The DNA sequence of canine RabW is shown in Fig. I.TheEMBL accession number is X56387.
Rabl2
Authors: Elferink Lisa A , Schellers Richard H 
Published: November 2023

Abstract
Rab12 was originally identified by screening a rat brain cDNA library under conditions of low stringency, using two previously identified cDNA clones, which shared significant homology to yeast Sec4 (Elferink et al. 1992; Ngsee et al. 1991; Goud etal. 1988). The nucleotide and deduced amino acid sequence of rat Rab12 is presented in Fig. 1. The GenBank accession number is M83676.
Rabl7
Authors: Liitcke Anne , Lehtonen Eero , Zerial Marino 
Published: November 2023

Abstract
A 1.6-kb Rab17 cDNA clone was isolated from an embryonic day 17 mouse kidney cDNA library using a polymerase chain reaction (PCR) fragment identified by Chavrier etal. (1992) as a probe. The size of the cDNA clone corresponded to the size of the Rabi 7 mRNA as determined by Northern blot (not shown). The nucleotide and deduced amino acid sequence of Rab17 as depicted in Fig. 1 (Lutcke etal. 1993) are available from the EMBL/GenBank/DDB under the accession number X70804.