bluuebunny/crossref_metadata_2025 huggingface dataset:
SEC11
Authors: öhni P B
Published: November 2023

Temperature-sensitive, conditionally-lethal sec11 mutants were isolated by a density enrichment protocol1. The best characterized sec11 allele is sec11-7. Within 15 min of a shift to the restrictive temperature of 37°C, sec11-7 mutant cells display a block in the signal peptide processing of invertase and acid phosphatase. The uncleaved precursor polypeptides accumulate as core-glycosylated proteins presumably within the lumen of the ER. The sec11 mutant is unique amongst the originally isolated set of sec mutants1, since it does not display any proliferation of membrane-bounded organelles. A sec11-llsec11-7 diploid strain is unable to sporulate3
SEC59
Authors: és G K ép
Published: November 2023

Temperature-sensitive, conditionally lethal sec59 mutants were selected on the basis of accumulation of inactive precursors of secreted proteins. Only one allele was obtained, sec59-1. At restrictive temperature, sec59-1 accumulates inactive and incompletely glycosylated forms of secretory proteins within the lumen of the endoplasmic reticulum.
DPM1
Authors: Orlean P
Published: November 2023

Dol-P-Man synthase catalyzes the transfer of mannose from the sugar nucleotide GDP-Man to the long-chain polyisoprenoid dolichyl phosphate (Dol-P). The 5. cerevisiae DPM1 gene was isolated using a screen that detected overproduction of Dol-P-Man synthase activity in colonies of yeast that had been transformed with a multicopy yeast genomic library1. Plasmids isolated from the overproducing 5. cerevisiae transformants also conferred Dol-P-Man synthase activity on £. coli when transformed into the bacteria, indicating that the structural gene for Dol-P-Man synthase had been isolated1.
ER α,1,2-mannosidase
Authors: “ Herscovics
Published: November 2023

Pulse-labeling studies showed that a specific Man8GlcNAc2 isomer is a transient intermediate during processing of NIinked oligosaccharides in 5. cerevisiae1, indicating the existence of a highly specific a-mannosidase associated with the ER, since this reaction occurs in sec18 cells at 37°C2. The specific enzyme was separated from the yeast vacuolar a-mannosidase3, and was first purified as a protepolytically-released enzymatically-active soluble form of approximately 60 kDa on SDS-PAGE4, and then as the intact 67-kDa membrane-bound form5 This specific αmannosidase does not work on aryl a-mannoside, is inhibited by dMNJ, and is Ca2+-dependent.
Protein translocation and maturation in the mammalian Er
Authors: blatt J Roth
Published: November 2023

Virtually all of the information that has provided our current understanding of how proteins are selected for insertion into the mammalian ER has been obtained from in vitro studies of protein import into canine pancreatic microsomes. A model describing our current understanding of the early events in the mammalian secretory process is shown in Figure 1. Co-translational targeting of a nascent secretory polypeptide to the ER membrane is initiated by the high affinity binding of signal recognition particle (SRP) to the amino-terminal signal sequence as the latter emerges from the large ribosomal subunit1. SRP is a cytosolic ribonucleoprotein complex1 that binds the signal sequence, the ribosome, and an ER-specific receptor protein - docking protein (DP, also called the SRP receptor) 23. Binding of SRP to a ribosome-associated nascent polypeptide induces a pause in polypeptide chain elongation and concurrently mediates a high affinity interaction with docking protein at the ER membrane1 Binding of SRP to docking protein promotes two further events: (i) the formation of a stable receptor-mediated interaction between the ribosome and the ER membrane, and (ii) the release of the nascent chain from SRP and its insertion into the ER membrane.
Signal recognition particle (SRP)
Authors: Zimmerman D L , Walter P
Published: November 2023

The particle is comprised of one molecule of 7SL RNA (about 300 nucleotides) and six distinct polypeptides3 The six SRP polypeptide chains are organized into four SRP proteins. These are two monomers, a 19 kDa polypeptide and a 54 kDa polypeptide, and two heterodimers, one composed of a 9 kDa and a 14 kDa polypeptide (p9/14), and the other comprised of a 68 kDa and a 72 kDa polypeptide (p68/72)4. The 7SL RNA spans the length of the SRP particle which, when viewed by electron microscopy, has a rodshaped, elongated structure5. SRP can be dissected biochemically into two structural and functional domains. One consists of p9/14 bound to the portions of 7SL RNA that contain the Alu sequences (see description of 7SL RNA below) and other (the S domain) consists of the remainder of the proteins and RNA6.
Calnexin
Authors: Bergeron J , Wada, I , Thomas D
Published: November 2023

The amino acid sequence deduced from the nucleotide sequences of two overlapping cDNA clones isolated from a dog pancreas cDNA library (GenBank accession number X53616) reveals a precursor protein of 593 amino acids including a 20 residue N-terminal signal sequence that is cleaved to generate the mature protein of 573 amino acids (calculated molecular mass 65,403). This mature protein contains an amphipathic sequence at residues 402-422, a potential transmembrane sequence at residues 463-484, and a cluster of acidic residues at the C-terminus whose presence may explain the abnormally high mobility (-90 kDa) of the protein during electrophoresis on SDS-PAGE.
GRP94
Authors: Green M
Published: November 2023

Murine GRP9411is encoded as an 802 amino acid precursor with a signal peptide of 21 amino acids. The calculated molecular weight of the mature protein is 90,096. There are six potential N-glycosylation sites in the murine GRP94 sequence. Only one of these, N196DT, is used under normal circumstances8,12. When GRP94 is over-expressed in COS cells11, however, a fraction of the molecules are hyperglycosylated in an all-or-none fashion at the three (OOH-terminal N-glycosylation sites12, N424VS, N460DT, and N481RT. This alteration in the pattern of glycosylation may reflect changes in the way in which GRP94 is translocated through the ER membrane during its synthesis.
7/Protein disulphide isomerase (PDI)
Authors: Freedman R B , Tuite M F
Published: November 2023

prolyl-4-hydroxylase subunit3.4; microsomal triglyceride transfer protein complex 58 kDa subunit5; ERp596, cellular thyroid hormone (T3) binding protein78; glycosylation site binding protein9; iodothyronine monodeiodinase. Protein chemical, enzymic and immunological data establish that the PDI polypeptide also acts as the subunit components of the tetrameric (a2 2) enzyme prolyl-4-hydroxylase34 and of the heterodimeric microsomal triglyceride transfer protein complex5 PDI was also isolated as ERp59, one of a set of abundant ER luminal proteins (ERps) in murine plasmacytoma cells. Purified PDI is readily affinity.
KBP-13
Authors: Sykes K
Published: November 2023

The nucleotide sequence of the FKBP-13 gene cloned from human cells (GenBank accession #M65128} predicts a protein of 141 amino acids that includes an N-terminal hydrophobic region thought to constitute a 21 residue signal peptide712. A (-terminal tetrapeptide (RTEL) may serve as a ER retention (or retrieval) sequence7 There is 55% amino acid sequence identity between the mature FKBP-13 proteins isolated from human cells and yeast, and 44% identity between FKBP-13 and the major cytoplasmic FKBP (FKBP-12) of human cells. A central region of marked homology among the several FKBP family members coincides with the drug binding and enzyme active site defined in FKBP-12.
SPC22/23
Authors: Shelness G
Published: November 2023

The amino acid sequence of SPC 22/23, deduced from cDNA clones2(GenBank accession number JO4067), predicts a protein of 180 amino acids and a calculated molecular mass of 20,314 Da. It contains a single N-linked, high mannose oligosaccharide chain at amino acid 14112. Although no sequence similarity was observed between SPC 22/23 and other proteins with known or suspected roles in proteolytic processing or translocation, identity was established with tryptic peptides derived from the hen oviduct signal peptidase glycoprotein (gp23)2·3
SPC21
Authors: Shclncss G
Published: November 2023

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

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

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.
SEC12
Authors: Nakano A
Published: November 2023

Temperature-sensitive conditional-lethal sec12 mutants were isolated by a density enrichment protocoI. Although three independent isolates are available, two of them (sec12-1 and sec12-4) have proved to contain the same point mutation in the coding region2.
SAR1
Authors: Nakano A
Published: November 2023

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.
VPS3
Authors: Raymond D K , Stevens T H
Published: November 2023

Total yeast extracts. Vps3p is expressed at low levels (-0.001% of total cellular protein). The discrepancy between the predicted and apparent molecular weight has not been investigated.
SRP54
Authors: Hann C C , Walter P
Published: November 2023

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

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

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

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

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

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

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

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

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

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.
Ras1p
Authors: Fasano Ottavio
Published: November 2023

The RAS1 gene was identified by screening a yeast DNA genomic library under low stringency with a mammalian RAS probe (DeFeo-Jones et al. 1983; Powers et al. 1984). GenBank accession numbers are K01970 and X00527.
Ste6
Authors: Hughes David A , Yamamoto Masayuki
Published: November 2023

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

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

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

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

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

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

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

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

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

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.
Mss4
Authors: Burton Janet , DeCamilli Pietro
Published: November 2023

Mss4 was originally identified in a genetic screen as a mammalian suppressor of the yeast secretory mutant sec4- 8, which contains a point mutation in the Sec4 protein (Burton et al. 1993). The goal of the study was to identify mammalian proteins involved in exocytosis that have been conserved in evolution using yeast genetics. Rat brain cDNAs were expressed in yeast using the expression vector pVT102U and Mss4 was isolated by its ability to restore growth to the sec4-8 strain at the restrictive temperature of 37°C (Fig. 1). The nucleotide sequence of Mss4 is shown in Fig. 2. The GenBank accession number is L10336.
Rabphilin-3A
Authors: Shirataki Hiromichi , Kaibuchi Kozo , Takai Yoshimi
Published: November 2023

Rabphilin-3A was purified from bovine brain and its cDNA was cloned based on the amino acid sequences from a bovine brain cDNA library (Shirataki etal. 1992, 1993). The nucleotide sequence of bovine rabphilin-3A and its deduced amino acid sequence are shown in Fig. 1. The GenBank accession number is D13613.
Ypt6p
Authors: Hengst Ludger , Grabowski Reiner , Gallwitz Dieter
Published: November 2023

YPT6 was identified and cloned using the fission yeast ryh 1 gene (Hengst et al. 1990) as hybridization probe. In contrast to its fission yeast homologue, the protein-coding region of YPT6 is continuous. The DNA sequence of YPT6 (Hengst et al., in preparation) is shown in Fig. 1. The GenBank accession number is X59598.
Ypt7p
Authors: Scheglmann Dietrich , Gallwitz Dieter
Published: November 2023

The YPT7 gene was identified by polymerase chain reaction (PCR)-based DNA amplification using genomic DNA and degenerate oligonucleotides corresponding to the sequences GVGKS/T and QIWDTAGQ conserved in Ypt/Rab proteins (Wichmann et al. 1992). The reading frame of YPT7 is continuous, the sequence of the gene (Wichmann et al. 1992) is shown in Fig. 1. The GenBank accession number isX68144.
Dss4p
Authors: Roberts Denise , Novick Peter
Published: November 2023

DSS4-1 suppresses the growth defect, the block in invertase secretion, and the accumulation of 100-nm secretory vesicles seen in sec4-8 cells at the restrictive temperature (Moya et al. 1993). Suppression is seen at 35°C, but not at 37°C whether DSS4-1 is present in single copy or overexpressed. DSS4-1 cannot suppress a deletion of SEC4 and cannot suppress the growth defect of ypt1-1. DSS4-1 has no effect on wild-type SEC4 cells.
Gyp6p (Ypt6-GAP)
Authors: Strom Molly , Vollmer Petra , Gallwitz Dieter
Published: November 2023

The GYP6 gene from S. cerevisiae encoding a GTPase activating protein was isolated by screening a yeast multi-copy genomic library for overexpression of the gene product. The DNA sequence is shown in Fig. 1. The EMBL accession number is X68506.
Arf1
Authors: Kahn Richard A
Published: November 2023

Bovine ARF1 was cloned by screening a bovine adrenal chromaffin cDNA library with an oligonucleotide probe, derived from partial protein sequencing of purified bovine brain ARF (Sewell and Kahn 1988; accession number J03275). The bovine clone was then used as a probe to obtain genomic yeast {Saccharomyces cerevisiae; Sewell and Kahn 1988; accession number P11076) and human (Bobak et al. 1989; Peng et al. 1989; accession number P32889/P10947) ARF1 cDNA clones.
Arf4
Authors: Kahn Richard A
Published: November 2023

ARF4 was cloned independently by two different laboratories and was originally given the name human ARF2, as it was the second human ARFcloned. This was later changed to ARF4 in case a human homologue of bovine ARF2 was discovered. A functional screen for genes that would promote the secretion of basic fibroblast growth factor (bFGF) by a human adrenal cortical carcinoma cell line dependent on this growth factor for growth in soft agar led to the isolation of a human ARF4 cDNA (Kahn et al.

1991). Human ARF4 cDNA (accession number P21371) was previously obtained by reverse transcription-polymerase chain reaction (RT-PCR) after initially cloning an ARF4 pseudogene (Monaco etal. 1990).
ArL3
Authors: Kahn Richard A
Published: November 2023

The partial cDNA sequence was first reported as one of many expressed sequence tags (EST) by Adams, et al (Adams et al. 1992; accession number M85466) as clone HFBCI57. Both strands of this clone were fully sequenced and 5’ RACE was performed to obtain the full-length open reading frame (Cavenagh etal. 1994). A rat homologue of ARL3 was obtained independently by workers in the laboratory of Dr Hans Joost (Cavenagh et al. 1994).
Secl2p
Authors: Barlowe Charles , Schekman Randy
Published: November 2023

The SEC12 gene was isolated by temperature-sensitive complementation of a sec12 mutant strain. Nucleotide sequence analysis of the structural gene predicts a 52-kDa protein with a 19 amino acid hydrophobic stretch near the C-terminus (Nakano eta/. 1988).
CD40 Ligand (CD40L)
Authors: Armitage R J
Published: November 2023

CD40 is a 50 kDa type I glycoprotein which is a member of the TNF receptor (TNFR) family. This group of related molecules includes both p60 and p80 forms of TNFR, the T cell activation antigens OX40, 4-1BB, CD27 and CD30, Fas antigen and a Shope fibroma virus-encoded TNFR homologue (Mallett and Barclay 1991). CD40 is expressed on B cells, follicular dendritic cells, thymic epithelium, mast cells, monocytes and some carcinomas (Clark 1990; Galy and Spits 1992; Alderson et al. 1993). Monoclonal antibodies (mAb) specific for CD40 induce a range of biological activities on human B cells including the induction of homotypic adhesion, short- and long-term proliferation in concert with various costimuli, production of lgE in the presence of IL-4 and production of other lg isotypes with IL-2 or IL-10 (Armitage et al. 1993a). In addition, ligation with CD40 mAb prevents the spontaneous apoptosis of germinal centre B cells in vitro (Liu et al. 1989). Murine and human ligands for CD40 have been identified and cloned.
Epidermal Growth Factor Receptor
Authors: Walker F , Burgess A W
Published: November 2023

The complete nucleotide sequences have been determined for the human EGFR (GenBank accession No X00588), human c-neu (GenBank accession No X03363), human EGFR B3 (HER3, Genbank accession No M29366) and human EGFR B4 (GenBank accession No L07868). Partial sequence information is available for the mouse and chicken EGFRs (Avivi eta/. 1991).
Fibroblast Growth Factors (FGFs)
Authors: Vainikka S , Mustonen T , Alitalo K
Published: November 2023

The first characterized members of the FGF family were aFGF and bFGF, which were purified as mitogens for fibroblasts from bovine pituitary.The lnt-2 oncogene was identified as a gene activated by mouse mammary tumour virus insertion. K-FGF and FGFS genes were identified by their ability to transform NIH 3T3 cells and FGF-6 was discovered because of its homology with the K-FGF/hst-1 gene. KGF was purified and cloned as a mitogen for cultured keratinocytes (see Burgess and Maciag 1989; Basilico and Moscatelli 1992), AIGF as an androgen-induced growth factor from the conditioned medium of a mouse mammary carcinoma cell line (Tanaka eta/. 1992) and GAF from the culture supernatant of a human glioma cell line (Miyamoto et al. 1993). A great advantage in the purification of FGFs has been their affinity for heparin.
Vascular Endothelial Growth Factor (VEGF) Receptors
Authors: Park J E , Ferrara N
Published: November 2023

Two tyrosine kinases have been recently identified as putative VEGF receptors (deVries et al. 1992; Terman et al. 1992a). The flt-1 (fms-like-tyrosine kinase; Shibuya et al. 1990) and KOR (kinase domain region; Terman et al. 1991) proteins have been shown to bind VEGF with high affinity. The overall amino acid sequence identity between the two proteins is 44 per cent. The murine homologue of KOR has been named flk-1 (fetal liver kinase; Matthews et al. 1991) and shares 85 per cent sequence identity with human KOR. For simplicity, the two receptors will be referred to as KOR/flk-1. Flt-1 and KOR/flk-1 each have a single hydrophobic leader peptide, a single transmembrane domain, seven immunoglobulin-like domains in its extracellular domain, and a consensus tyrosine kinase sequence which is interrupted by a kinase-insert domain. Flt-1 and KDR share 30 per cent sequence identity with c-fms, a known tyrosine kinase receptor for M-CSF (CSF-1).
Escherichia coli DnaK
Authors: Buchberger A , Bukau B
Published: November 2023

The dnaK gene is the promoter proximal gene of the dnaK dnaJ operon located at 0.3 minutes on the E. coli map. The nucleotide sequence of E. coli dnaK (GenBank accession number K01298 for strain K12; DDBJ accession number D10765 for strain B) encodes a 69-kDa protein of 638 residues (Bardwell, Craig, 1984). The N-terminal formylmethionine is cleaved off in vivo.
Saccharomyces cerevisiae Ssa proteins
Authors: Ziegelhoffer T , Craig E A
Published: November 2023

The SSA1-4 genes (initially known as YG100, YG102, YG106, YG107, respectively) were isolated by virtue of their high degree of homology to Drosophila HSP70 genes (Ingolia etal., 1982).
Saccharomyces cerevisiae Kar2p
Authors: Craig E A
Published: November 2023

The KAR2 gene was isolated initially in a selection for karyogamy (nuclear fusion) defective mutants in yeast (Polaina, Conde, 1982; Rose et al., 1989). Subsequent to the original genetic identification, KAR2 was identified independently by several laboratories using DNA probes homologous to HSP70 (Craig et al., 1987; Normington etal., 1989; Nicholson etal., 1990).
Plant BiP proteins
Authors: Gillikin J W , Boston R S
Published: November 2023

b-70 (Galante et al., 1983), luminal binding protein (Denecke etal., 1991). Plant BiP was originally purified from maize kernels using procedures that employed ATP-agarose affinity chromatography (Fontes et al., 1991; Marocco et al., 1991). Analysis of affinity purified protein by two-dimensional gel electrophoresis revealed the presence of three polypeptides (Fontes et al., 1991). However, only two of these cross-react with anti-HDEL antibody (Boston et al., 1991) .
Drosophila melanogaster Hsc3p
Authors: Rubin A , Palter K
Published: November 2023

The nucleotide sequence for Drosophila HSC3 (Rubin et al., 1993) was determined from both genomic, larval cDNA clones (GenBank accession numbers L01498, L01499). The genomic clone was shown to contain introns of 1.98, 0.37 kb. The cDNA has a single open reading frame (ORF) of 1968 bp that would encode a protein of 656 amino acids, including an 18-residue N-terminal hydrophobic signal sequence, a C-terminal retrieval tetrapeptide, KDEL (Rubin et al., 1993).
Fish HSP70 proteins
Authors: Hightower L E , Ryan J A , Norris C E
Published: November 2023

Fish Hsp70s were originally identified as proteins induced in cultured fish cells by exposure to heat, heavy metal ions or sodium arsenite. Initial biochemical characterizations were done using denaturing polyacrylamide gel electrophoresis (Heikkila et al., 1982; Kothary, Candido, 1982).
Mammalian BiP
Authors: Gething M -J
Published: November 2023

The nucleotide sequences of BiP cDNAs cloned from mammalian species (Munro, Pelham, 1986; Ting etal., 1987; Ting, Lee, 1988; Kozutsumi et al., 1989) (GenBank accession numbers M19645, M17169) predict a protein of 635 amino acids that includes an 18-residue N-terminal signal sequence,, a C-terminal tetrapeptide (Lys-Asp-Glu—Leu or KDEL) required for retrieval of BiP molecules that leave the ER (Pelham, 1989). Clusters of acidic amino acids, thought to be involved in the low affinity, high capacity Ca2+-binding activity of the molecule (Macer, Koch, 1988), are found at both the N-, C-termini of the molecule.
Saccharomyces cerevisiae Sse1, Sse2 proteins
Authors: Mukai H , Shuntoh H , Kuno T
Published: November 2023

Complementary DNAs encoding Sse1, Sse2 proteins were isolated from a S. cerevisiae expression library using antisera made against a yeast calmodulin-binding fraction (Mukai etal., 1993). The SSE1 gene was also isolated as a multicopy suppressor of the heat shock-sensitive phenotype of the ira1 mutation, which causes hyperactivation of the RAS-cAMP pathway (Shirayama et al., 1993).
The sea urchin egg receptor for sperm
Authors: Stears R L , Just, M L , Lennarz WJ
Published: November 2023

A 70 kDa glycoprotein fragment of the egg receptor for sperm was isolated by endolysyl proteinase C digestion of dejellied Strongylocentrotus purpuratus eggs, followed by DEAE, gel exclusion chromatography. The receptor glycoprotein fragment was detected by its ability to inhibit fertilization in competitive fertilization bioassays (Foltz, Lennarz, 1990). A polyclonal antibody generated against the 70 kDa fragment was used to screen an ovary/oocyte expression cDNA library in order to clone the receptor (Foltz et al., 1993).
Mammalian Hsp70h
Authors: Dyer K D , Rosenberg H F
Published: November 2023

hsp70RY (Fathallah et al., 1993, Dyer, Rosenberg, 1994, Lee-Yoon etal., 1995) The cDNA encoding Hsp70h was isolated from a human EBV-transformed B cell cDNA library using a CD18-derived cDNA probe (Fathallah et al., 1993). The open reading frame was later confirmed, further characterized by Dyer, Rosenberg (1994).
Escherichia coli DnaJ
Authors: Wawrzynow A , Zylicz M
Published: November 2023

The dnaJ gene is located in an operon with dnaK at 0.3 minutes on the E. coli genetic map (Georgopoulos et al., 1994). The nucleotide sequence of the dnaJ gene (GenBank accession number M12565) predicts a protein of 375 amino acids (Bardwell et al., 1986; Ohki et al., 1986), which is highly homologous to DnaJ-like proteins from the cytosol, endoplasmic reticulum, mitochondria of eukaryotic cells.
Escherichia coli RcsG
Authors: Kelley W L , Georgopoulos C
Published: November 2023

RcsG has also been isolated as DjIA (Clarke et al., 1966), a multicopy suppressor conferring resistance to the anticalmodulin drug, W7. Two bacterial genes having significant homology to rcsG have also been described. The gene mucZ (GenBank accession numbers L42518, P44607) of Coxiella burnetti shows 42% amino acid identity to rcsG, and, when present in a multicopy vector, it confers mucoidy upon the E. coli host. Preliminary characterization of C. burnetti mucZ in E. coli suggests that it may indeed encode a functional homolog of RcsG as it can positively stimulate the cps operon, requires DnaK, GrpE for this activity (Zuber et al., 1995).
DnaJ-like proteins from leek: Ldj1, Ldj2
Authors: Bessoule J -J
Published: November 2023

Four different Dna J proteins have been reported in the yeast Saccharomyces cerevisiae (for review see Silver, Way, 1993); in plant cells, only proteins homologous to one of them (Ydj1) have been described: Anj1 (see previous entry, p. 112), LdJ1, Ldj2, Csdna J1, Atj2 from Atriplex nummularia. Allium porrum, Cucumis sativus, Arabidopsis thaliana, respectively (Bessoule, 1993; Preisig- Muller, Kindi, 1993; Zhu et al., 1993a; Bessoule et al.
Human neurone-specific Hsj1 proteins
Authors: Cheetham M E , Tighe M
Published: November 2023

Human neurone-specific DnaJ-like proteins Hsj1 proteins were initially identified by immunoscreening an Alzheimer’s disease brain expression cDNA library using a polyclonal antiserum raised to a preparation of paired helical filaments (PHF), one of the pathological hallmarks of Alzheimer’s disease. However, to date we have been unable to confirm the association of Hsjl proteins with PHF (Cheetham etal., 1992).
The GrpE family of proteins — an overview
Authors: Deloche O , Ang D , Georgopoulos C
Published: November 2023

The E. coli grpE gene was first identified by Saito, Uchida (1977) in a massive mutant hunt, designed to identify genes whose products are essential for bacteriophage A replication. The particular selection employed was bacterial survival at 42°C in a lysogenic strain that carried a thermolabile Ad857 repressor. The grpE280 mutation was thereby isolated, defining the grpE gene (Saito, Uchida, 1977). Other prokaryotic grpE-Wke genes were identified as being part of the dnaK operon (Wetzstein, Schumann, 1990). A grpE gene has also been detected in Methanosarcina mazei as being part of the dnaK operon (Conway de Macario etal., 1994).