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D Y Thomas

Publications and source records attributed to D Y Thomas.

At least 91 records · Page 5Linked to original sources
PubMed1995

Redesigning the active site of Geotrichum candidum lipase.

Attempts to engineer enzymes with unique catalytic properties have largely focused on altering the existing specificities by reshaping the substrate binding pockets. Few experiments have aimed at modifying the configuration of the residues essential for catalysis. The difference in the topological location of the triad acids of Geotrichum candidum lipase (GCL) and the catalytic domain of human pancreatic lipase (HPL), despite great similarities in their topologies and 3-D structures, suggest that these are related enzymes whose catalytic triads have been rearranged in the course of evolution (Schrag et al., 1992). In this study we prepared a double mutant GCL in which the catalytic triad acid is shifted to the position equivalent to the location of the triad acid of HPL. The double mutant maintains approximately 10% of the wild type activity against triglycerides and the fluorogenic ester 4-methylumbelliferyl-oleate. The only significant differences between the 3-D structures of the double mutant and wild type GCL are at the mutated sites. Even the water structure in the region of the triad is unchanged. The hydrogen bonding pattern of the catalytic triad of the double mutant is very similar to that of pancreatic lipase. The acid of the double mutant is stabilized by only two hydrogen bonds, whereas three hydrogen bonds are observed in the wild type enzyme. These results strongly support the hypothesis that the pancreatic lipases are evolutionary switchpoints between the two observed arrangements of the catalytic triads supported by the alpha/beta hydrolase fold and suggest that this fold provides a stable protein core for engineering enzymes with unique catalytic properties.

Amino Acid Sequence↗
PubMed1994

Molecular characterization of SIG1, a Saccharomyces cerevisiae gene involved in negative regulation of G-protein-mediated signal transduction.

Two recessive mutations in the Saccharomyces cerevisiae SIG1 (suppressor of inhibitory G-protein) gene have been identified by their ability to suppress the signalling defect of dominant-negative variants of the mating response G-protein beta-subunit. The mutations and deletion of SIG1 enhance the sensitivity of the cells to pheromone and stimulate the basal transcription of a mating specific gene, FUS1, suggesting that Sig1p plays a negatively regulatory role in G beta gamma-mediated signal transduction. An additional function of Sig1p in vegetatively growing cells is suggested by the finding that the mutations and deletion of SIG1 cause temperature-sensitive growth defects. The SIG1 gene encodes a protein with a molecular weight of 65 kDa that contains at the amino-terminus two zinc finger-like sequence motifs. Epistasis experiments localize the action of Sig1p within the pheromone signalling pathway at a position at or shortly after the G-protein. We propose that Sig1p represents a novel negative regulator of G beta gamma-mediated signal transduction.

Amino Acid Sequence↗
PubMed1994

Polymorphism in the lipase genes of Geotrichum candidum strains.

The fungus Geotrichum candidum produces extracellular lipases. Purification and characterization of different lipase isoforms from various G. candidum strains is difficult due to the close physical and biochemical properties of the isoforms. Consequently, the characterization of these enzymes and their substrate specificities has been difficult. We have determined the lipase genes present in four strains of G. candidum (ATCC 34614, NRCC 205002, NRRL Y-552 and NRRL Y-553) by molecular cloning and DNA sequencing. Each strain contains two genes similar to the previously identified lipase I and lipase II cDNAs. Our data suggest that no other related lipase genes are present in these strains. Each lipase-gene family shows sequence variation (polymorphism) that is confirmed by Southern-blot analysis. This polymorphism and the sequence differences between lipase I and lipase II have been localized within the previously determined three-dimensional structure of lipase II. Although most of the amino acid substitutions are located on the protein surface, some are present in structural features possibly involved in determining substrate specificity.

Amino Acid Sequence↗
PubMed1994

Secretion, purification and characterization of a soluble form of the yeast KEX1-encoded protein from insect-cell cultures.

The Saccharomyces cerevisiae KEX1 gene encodes a carboxypeptidase involved in the C-terminal processing of the lysine and arginine residues from the precursors of K1 and K2 killer toxins and alpha-factor (mating pheromone). In order to produce large quantities of this unique carboxypeptidase for structural studies, a functional soluble form was obtained by deleting 224 amino acids from the C-terminus of the KEX1-encoded protein which includes a putative membrane-spanning domain. The resulting truncated KEX1 gene (KEX1 delta) has been expressed in the baculovirus/insect cell system. The protein (Kex1 delta p) is efficiently secreted into the culture medium and was purified to apparent homogeneity with a yield of approximately 4 mg/l culture. Kex1 delta p is a glycoprotein with a molecular mass of 56 kDa, its N-terminal sequence is identical to that of the full-length membrane-associated form of the enzyme [Latchinian-Sadek, L. & Thomas, D. Y. (1993) J. Biol. Chem. 268, 534-540], and like the full-length enzyme it is not made as a proenzyme. For the soluble enzyme form, the optimum pH for activity was 5.5-6.0, and the apparent pI value of the protein determined by isoelectric focusing was 4.2. The enzyme cleaves arginine from the C-terminus of the synthetic peptide benzoyl-Phe-Ala-Arg with Km 335 microM and Vmax 282 mumol.min-1 x mg protein-1. Insect-cell-derived Kex1 delta p processes alpha-factor-Lys-Arg, a known natural substrate, to mature active alpha-factor in a manner similar to the membrane-associated full-length enzyme. This secreted form of the enzyme is a convenient source for the isolation of substantial quantities of the pure enzyme for detailed kinetic and structural studies.

Amino Acid Sequence↗
PubMed1994

Control of expression, glycosylation, and secretion of HIV-1 gp120 by homologous and heterologous signal sequences.

The HIV-1 gp120 signal sequence of 30 amino acids is longer than most glycoprotein signal sequences and contains an average of 5 positively charged amino acids. The HIV-1 gp120 gene with its natural signal sequence expressed in any prokaryotic or eukaryotic expression systems showed extremely low levels of synthesis and secretion. However, deletion of the HIV-1 gp120 signal sequence results in production of large quantities of a nonglycosylated form of gp120 in Spodoptera frugiperda cells. Substitution of the gp120 natural signal sequences with the signal sequences from honeybee mellitin or murine interleukin 3 promotes a high level of expression of a glycosylated form of gp120 and efficient secretion. These heterologous signal sequences contain one (mellitin) or no (IL-3) positively charged amino acids and led us to investigate the role of the positively charged amino acids in the signal sequence of HIV-1 gp120. Four charge-altered forms of the gp120 signal sequence of HIV-1 were constructed by site-directed mutagenesis in which the positively charged amino acids were sequentially substituted with neutral amino acids. The results of these experiments showed that the expression and secretion of gp120 was progressively increased by eliminating the positively charged amino acids in a stepwise fashion. However, the substitution of all positively charged amino acids resulted in the accumulation of nonglycosylated gp120 within the cells with decreased amounts of the glycosylated form of gp120. These results demonstrate that the positively charged amino acids in the signal sequence of HIV-1 gp120 are key factors in determining its poor expression and secretion. Analyses of intracellular transport and folding of gp120 further indicate that the presence of a highly charged, uncleaved signal sequence is an important factor limiting transport of gp120 from the rough ER to the Golgi apparatus.

Amino Acid Sequence↗
PubMed1994

Cleavage of prosomatostatins by the yeast Yap3 and Kex2 endoprotease.

A previous in vivo study implicated the YAP3 and KEX2 genes in the proteolytic maturation of anglerfish prosomatostatins which were heterologously expressed in the yeast Saccharomyces cerevisiae. In the present report, we have determined the cleavage specificity of these enzymes by incubating them in vitro with synthetic peptides mimicking the potential processing sites present in the somatostatin precursors and with full length prosomatostatin I. The Yap3 enzyme was prepared from a membrane fraction of a YAP3-overexpressing yeast, and a soluble form of Kex2 obtained from the culture medium of insect cells which had been infected with a recombinant baculovirus expressing the KEX2 gene. The identity of the cleavage products was confirmed by amino acid analysis. Our results show that both endoproteases generate mature SRIF-28 from prosomatostatin-II but that only Yap3 can process the homologous monobasic cleavage site (ie single arginine residue) found in prosomatostatin-I. Both enzymes were also shown to recognize the Arg-Lys doublet found in prosomatostatin-I producing a lysine-extended form of SRIF-14, which indicates that cleavage occurred C-terminal to the arginine residue. In addition, Kex2 also hydrolyzed C-terminal to the Pro-Arg motif to release a tripeptide-extended form of SRIF-14. However, neither endoprotease could cleave after the Arg-Lys doublet to release mature SRIF-14. Taken together, our results indicate that the yeast Kex2 and Yap3 endoproteases have distinct, though overlapping, substrate specificities. The results also strongly support the role of Yap3 as a proprotein convertase which perhaps defines a new family of processing enzymes.

Amino Acid Sequence↗
PubMed1994

Calnexin: a membrane-bound chaperone of the endoplasmic reticulum.

Calnexin is a new type of molecular chaperone that interacts with many nascent membrane and soluble proteins of the secretory pathway. Calnexin is unrelated to molecular chaperones of the Hsp60, Hsp70 and Hsp90 families, and is further distinguished from them in that it is an integral membrane protein. One of its demonstrated functions is the retention of incorrectly or incompletely folded proteins, suggesting that calnexin is a component of the quality control system of the endoplasmic reticulum.

Calcium-Binding Proteins↗
PubMed1994

Site-directed mutations altering the CAAX box of Ste18, the yeast pheromone-response pathway G gamma subunit.

The STE18 gene encodes the gamma subunit of the G protein which functions in the Saccharomyces cerevisiae pheromone-response pathway. The STE18 gene product undergoes a post-translational processing at the carboxyl terminus directed by the CCAAX box motif CCTLM110. A variety of site-directed mutations of this sequence have been constructed to test the role of this motif on Ste18 function. Mutations which change or eliminate the cysteine at position 107 abolish Ste18-dependent mating, and thus the cysteine (C107) is essential for Ste18 function. However, inactivation of the prenyltransferase by disruption of DPR1 has only a minor effect on Ste18-dependent mating. Mutation of cysteine 106 to serine significantly reduces but does not eliminate Ste18 function. Deletion of the C-terminal TLM sequence or modification of the ultimate methionine to lysine, arginine or leucine, all changes which do not affect the CAAX box cysteines, have only minor effects on Ste18-dependent mating. Intriguingly, these latter mutations dramatically compromise Ste18 function in cells which are deleted for Gpa1, the alpha subunit of the G protein. In addition, overexpression of these mutant versions of STE18 causes a dominant negative phenotype and inhibits the constitutive mating response generated by GPA1 deletion in cells which contain a functional STE18 gene. These results suggest that the C terminus of Ste18 and the Gpa1 protein have overlapping roles in some aspect of yeast G protein function such as membrane targeting.

Alkyl and Aryl Transferases↗
PubMed1994

Functional expression of P-glycoprotein in Saccharomyces cerevisiae confers cellular resistance to the immunosuppressive and antifungal agent FK520.

We have recently reported that expression in yeast cells of P-glycoprotein (P-gp) encoded by the mouse multidrug resistance mdr3 gene (Mdr3) can complement a null ste6 mutation (M. Raymond, P. Gros, M. Whiteway, and D. Y. Thomas, Science 256:232-234, 1992). Here we show that Mdr3 behaves as a fully functional drug transporter in this heterologous expression system. Photolabelling experiments indicate that Mdr3 synthesized in yeast cells binds the drug analog [125I]iodoaryl azidoprazosin, this binding being competed for by vinblastine and tetraphenylphosphonium bromide, two known multidrug resistance drugs. Spheroplasts expressing wild-type Mdr3 (Ser-939) exhibit an ATP-dependent and verapamil-sensitive decreased accumulation of [3H]vinblastine as compared with spheroplasts expressing a mutant form of Mdr3 with impaired transport activity (Phe-939). Expression of Mdr3 in yeast cells can confer resistance to growth inhibition by the antifungal and immunosuppressive agent FK520, suggesting that this compound is a substrate for P-gp in yeast cells. Replacement of Ser-939 in Mdr3 by a series of amino acid substitutions is shown to modulate both the level of cellular resistance to FK520 and the mating efficiency of yeast mdr3 transformants. The effects of these mutations on the function of Mdr3 in yeast cells are similar to those observed in mammalian cells with respect to drug resistance and transport, indicating that transport of a-factor and FK520 in yeast cells is mechanistically similar to drug transport in mammalian cells. The ability of P-gp to confer cellular resistance to FK520 in yeast cells establishes a dominant phenotype that can be assayed for the positive selection of intragenic revertants of P-gp inactive mutants, an important tool for the structure-function analysis of mammalian P-gp in yeast cells.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1994

Genetic identification of residues involved in association of alpha and beta G-protein subunits.

The GPA1, STE4, and STE18 genes of Saccharomyces cerevisiae encode the alpha, beta, and gamma subunits, respectively, of a G protein involved in the mating response pathway. We have found that mutations G124D, W136G, W136R, and delta L138 and double mutations W136R L138F and W136G S151C of the Ste4 protein cause constitutive activation of the signaling pathway. The W136R L138F and W136G S151C mutant Ste4 proteins were tested in the two-hybrid protein association assay and found to be defective in association with the Gpa1 protein. A mutation at position E307 of the Gpa1 protein both suppresses the constitutive signaling phenotype of some mutant Ste4 proteins and allows the mutant alpha subunit to physically associate with a specific mutant G beta subunit. The mutation in the Gpa1 protein is adjacent to the hinge, or switch, region that is required for the conformational change which triggers subunit dissociation, but the mutation does not affect the interaction of the alpha subunit with the wild-type beta subunit. Yeast cells constructed to contain only the mutant alpha and beta subunits mate and respond to pheromones, although they exhibit partial induction of the pheromone response pathway. Because the ability of the modified G alpha subunit to suppress the Ste4 mutations is allele specific, it is likely that the residues defined by this analysis play a direct role in G-protein subunit association.

Amino Acid Sequence↗
PubMed1993

Cloning and expression of Geotrichum candidum lipase II gene in yeast. Probing of the enzyme active site by site-directed mutagenesis.

The three-dimensional structure of lipase II of Geotrichum candidum strain ATCC34614 (GCL II) has provided insights with respect to the nature of the catalytic machinery of lipases. To support these structural observations, we have carried out an analysis of GCL II by mutagenesis. The gene encoding lipase II of Geotrichum candidum strain ATCC34614 (GCL II) was amplified using the polymerase chain reaction, cloned, and sequenced. The intronless lipase gene was expressed and secreted from Saccharomyces cerevisiae at approximately 5 mg/liter of culture. Recombinant GCL II was purified by immunoaffinity chromatography and characterized using a combination of substrates and independent analytical methods. The recombinant enzyme and the enzyme isolated from its natural source have comparable specific activities against triolein of about 1000 mumol of oleic acid released/min/mg of protein. The putative catalytic triad Ser217-His463-Glu354 was probed by site-directed mutagenesis. The substitution of Ser217 by either Cys or Thr and of His463 by Ala led to a complete elimination of the activity against both triolein and tributyrin. Substitution of Glu354 by either Ser, Ala or Gln renders the enzyme inactive and also perturbs the enzyme stability. However, the enzyme with the conservative replacement Glu354 Asp is stable and displays only a small decrease of triolein activity but a 10-fold decrease in activity against tributyrin. There was no appreciable difference in esterase activity between the native, recombinant wild type, and Glu354 Asp mutant. These results confirm that the triad formed by Ser217-Glu354-His463 is essential for catalytic activity. They also show that the active site of GCL II is more tolerant to a conservative change of the carboxylic side chain within the triad than are other hydrolases with similar catalytic triads.

Aspartic Acid↗
PubMed1993

Association of folding intermediates of glycoproteins with calnexin during protein maturation.

Calnexin, an endoplasmic reticulum transmembrane protein, represents a new type of molecular chaperone that selectively associates in a transient fashion with newly synthesized monomeric glycoproteins in HepG2 cells. Calnexin only recognizes glycoproteins when they are incompletely folded. Dissociation of glycoproteins from calnexin occurs at different rates and is related to the time taken for their folding, which may then initiate their differential transport rates from the endoplasmic reticulum.

Albumins↗
PubMed1993

Processing of Kex2 pro-region at two interchangeable cleavage sites.

In Saccharomyces cerevisiae, the Kex2 endoprotease (Kex2p) is required for the proteolytic maturation of alpha-pheromone and also for the removal of its own pro-region. Kex2p is specific for pairs of basic amino acid residues. Two putative processing sites are present in the pro-region of Kex2p. We have expressed processing site mutants of Kex2p and assayed the production of active Kex2p. Mutations affecting either putative cleavage site do not alter the activity. However, mutations affecting both sites led to a reduction in both Kex2 activity and the amount of protein. These results suggest that removal of Kex2p pro-peptide is required for the production of a stable enzyme and can occur at either processing site.

Enzyme Stability↗
PubMed1993

Functional expression of human cathepsin S in Saccharomyces cerevisiae. Purification and characterization of the recombinant enzyme.

A cDNA encoding the human lysosomal cysteine proteinase cathepsin S precursor has been expressed in yeast using the pVT100-U expression vector containing the alpha-factor promoter. The procathepsin S gene was expressed either as a fusion protein with the pre-region or with the prepro-region of the yeast alpha-factor precursor gene. Following in vitro processing both constructs gave an identical active mature enzyme with a molecular weight of 24,000. After prolonged cultivation of the cells the recombinant protein is also found as an active proteinase in the culture supernatant. The precursor can be activated in vitro at pH 4.5 and 40 degrees C under reducing conditions. The in vitro activated enzyme has a 6-amino acid NH2-terminal extension when compared with the native bovine enzyme. The purified enzyme displays a bell-shaped pH activity profile with a pH optimum of 6.5 and pK values of 4.5 and 7.8. The isoelectric point of the recombinant human cathepsin S is between 8.3 and 8.6 and about 1.5 pH units higher than for the bovine enzyme. The kinetic data for several synthetic substrates and inhibitors reveal a preference for smaller amino acid residues in the binding subsites S2 and S3 of cathepsin S. Like the bovine enzyme, the recombinant human cathepsin S is characterized by a broader range of pH stability (pH 5-7.5) than cathepsins B and L.

Base Sequence↗
PubMed1993

Expression, purification, and characterization of the yeast KEX1 gene product, a polypeptide precursor processing carboxypeptidase.

The Saccharomyces cerevisiae KEX1 gene encodes a protease with carboxypeptidase B-like activity involved in K1 and K2 killer toxins and alpha-factor (mating pheromone) precursors processing. The gene has been expressed using the baculovirus/insect cell system, and the KEX1 encoded protein (Kex1p) was purified to apparent homogeneity from detergent-solubilized membrane preparations of insect cells infected with the recombinant virus. The specific activity of the enzyme was enriched 126-fold as compared with the cell lysate, with a recovery of 29%. The NH2-terminal sequence of the purified active enzyme was identical to the predicted sequence after the removal of the signal peptide. This provides evidence that Kex1p, at least in insect cells, is not made as a proenzyme. The optimum pH for activity was 6.0, and the apparent pI value of the protein was below pH 3.0. The enzyme cleaves arginine or lysine from the COOH terminus of synthetic peptides: benzoyl-Phe-Ala-Arg (Km = 284 microM), furylacryloyl (fa)-Ala-Arg (Km = 516 microM), and fa-Ala-Lys (Km = 962 microM). The kinetic data obtained reveals that Kex1p preferentially cleaves the COOH-terminal arginine of peptides over the COOH-terminal lysine. Insect-derived Kex1p processes alpha-factor-Lys-Arg, its known natural substrate, to mature active alpha-factor, and this maturation event takes place in a sequential manner. Furthermore, the enzyme expresses very high affinity for the 15-amino acid-long peptide, alpha-factor-Lys-Arg (Ki = 22 microM), and somewhat lower affinity for the heptapeptides [Leu]enkephalin-Arg-Arg,-Arg-Lys, and [Met]enkephalin-Lys-Lys (Ki = 45, 57, and 81 microM, respectively). The data demonstrate that processing at the COOH terminus of the peptides tested stops after the cleavage of the Arg and/or Lys residues. The specificity of the enzyme for COOH-terminal basic amino acid residues of the peptides used in this study and its high affinity for alpha-factor-Lys-Arg confirms the role that Kex1p plays in polypeptide precursor processing in yeast.

Amino Acid Sequence↗
PubMed1993

Isolation and characterization of S. cerevisiae mutants defective in somatostatin expression: cloning and functional role of a yeast gene encoding an aspartyl protease in precursor processing at monobasic cleavage sites.

The peptide somatostatin exists as two different molecular species. In addition to the most common form, somatostatin-14, there is also a fourteen amino acid N-terminally extended form of the tetradecapeptide, somatostatin-28. Both peptides are synthesized as larger precursors containing paired basic and monobasic amino acids at their processing sites, which upon cleavage generate either somatostatin-14 or -28, respectively. In some species of fish two distinct, but homologous, precursors (prosomatostatin-I and -II) give rise to somatostatin-14 and -28, respectively. Whereas anglerfish prosomatostatin-II was previously shown to release exclusively somatostatin-28, the yeast Saccharomyces cerevisiae proteolytically matures the homologous prosomatostatin-I precursor to somatostatin-28 and -14 as well as to a lysine-extended form of somatostatin-14. The Kex2 endoprotease appears to be essential for the formation of lysine somatostatin-14 and is involved either directly or indirectly in the release of mature somatostatin-14. The isolation of yeast mutants defective in somatostatin-28 expression (sex mutant) allowed the cloning of a non-essential gene, which encodes an aspartyl protease, whose disruption severely affects the cleavage of mature somatostatin-28 from both somatostatin precursors. We conclude that two distinct endoproteases, which demonstrate some cross specificity in vivo, are involved in the proteolytic maturation of prosomatostatin at mono- and dibasic processing sites in yeast.

Amino Acid Sequence↗
PubMed1993

Cloning of Saccharomyces cerevisiae STE5 as a suppressor of a Ste20 protein kinase mutant: structural and functional similarity of Ste5 to Far1.

The beta and gamma subunits of the mating response G-protein in the yeast Saccharomyces cerevisiae have been shown to transmit the mating pheromone signal to downstream components of the pheromone response pathway. A protein kinase homologue encoded by the STE20 gene has recently been identified as a potential G beta gamma target. We have searched multicopy plasmid genomic DNA libraries for high gene dosage suppressors of the signal transduction defect of ste20 mutant cells. This screen identified the STE5 gene encoding an essential component of the pheromone signal transduction pathway. We provide genetic evidence for a functional interrelationship between the STE5 gene product and the Ste20 protein kinase. We have sequenced the STE5 gene, which encodes a predicted protein of 917 amino acids and is specifically transcribed in haploid cells. Transcription is slightly induced by treatment of cells with pheromone. Ste5 has homology with Far1, a yeast protein required for efficient mating and the pheromone-inducible inhibition of a G1 cyclin, Cln2. A STE5 multicopy plasmid is able to suppress the signal transduction defect of far1 null mutant cells suggesting that Ste5, at elevated levels, is able functionally to replace Far1. The genetically predicted point of function of Ste5 within the pheromone signalling pathway suggests that Ste5 is involved in the regulation of a G beta gamma-activated protein kinase cascade which links a G-protein coupled receptor to yeast homologues of mitogen-activated protein kinases.

Adaptor Proteins, Signal Transducing↗