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S Y Yang

Publications and source records attributed to S Y Yang.

At least 91 records · Page 5Linked to original sources
PubMed1997

The pentanucleotide ATTGG, the "inverted CCAAT," is an essential element for HLA class I gene transcription.

The HLA class I genes, HLA-A, -B, and -C, contain an inverted CCAAT sequence (ATTGG) located 20 bp upstream of the canonical CCAAT and approximately 70 bp upstream of the transcription initiation site. We have investigated the transcriptional function of the class I inverted CCAAT sequence using the HLA-normal cell line, HeLa. Deletion, mutation, or inversion of the inverted CCAAT sequence abrogated or reduced the activity of the class I promoter, as assessed by luciferase reporter gene assays in transient gene expression experiments. This activity coincided with occupancy of the inverted CCAAT motif, as tested by electrophoretic mobility shift assays using the wild-type sequence and mutated variants of the sequence. The ATTGG-binding protein was not CP2, NF-1, or other known CCAAT-binding proteins, but the complex may contain a CP1/NF-Y-like protein. Our results indicate that this inverted CCAAT sequence is an essential element for the expression of HLA class I genes and that its transcriptional activity depends upon the sequence, position, and orientation of the pentanucleotide.

Base Sequence↗
PubMed1997

Importance of the gamma-carboxyl group of glutamate-462 of the large alpha-subunit for the catalytic function and the stability of the multienzyme complex of fatty acid oxidation from Escherichia coli.

His450 of the large alpha-subunit of the multienzyme complex of fatty acid oxidation from Escherichia coli was recently identified as an essential catalytic residue of L-3-hydroxyacyl-CoA dehydrogenase [He, X-Y., & Yang, S.-Y. (1996) Biochemistry 35, 9625-9630]. To explore the roles of acidic residues in the dehydrogenase catalysis, every conserved acidic residue in the dehydrogenase functional domain except for those in the NAD-binding motif was replaced with alanine. The resulting mutant complexes were overproduced and characterized. Their component enzymes other than the dehydrogenase were affected very slightly. Removal of the beta-carboxyl group of Asp524 and Asp542 caused only a 3- and 4-fold, respectively, decrease in the catalytic efficiency of the dehydrogenase, thereby showing that their involvement in the dehydrogenase catalysis was limited. In contrast, the alpha/Glu462-->Ala mutant complex showed a greater than 160-fold reduction in the kcat of the dehydrogenase in the forward direction without a significant change of the k(m) for the substrate. The catalytic properties of the alpha/Glu462-->Gln mutant complex were found to be similar to those of the alpha/Glu462-->Ala mutant complex except that the kcat of the dehydrogenase in the backward direction was about 4-fold lower and the Km for the substrate of the thiolase was 6-fold higher. It is concluded that the negative charge of the gamma-carboxyl group of Glu462, but not its ability to form a hydrogen bond, is critical for its interaction with His450, thereby assisting in the catalysis of the dehydrogenase. The pKa of His450 in the E.NADH binary complex was virtually unchanged by the replacement of Glu462 with Ala or Gln. It seems that the binding of substrate is necessary for forming a strong interaction between His450 and Glu462 with the result that the electroneutrality in the active site is maintained and the activation energy of the reaction is lowered. Additionally, the negative charge of Glu462 increases the thermostability of the multienzyme complex.

3-Hydroxyacyl CoA Dehydrogenases↗
PubMed1997

Locus-specific conservation of the HLA class I introns by intra-locus homogenization.

The protein-coding sequences of the major histocompatibility complex (MHC) genes are characterized by extraordinarily high polymorphism, apparently maintained by balancing selection, which favors diversity in the peptide-binding domains of the MHC glycoproteins. Here we report that the introns flanking the polymorphic exons of the human MHC class I loci HLA-A, -B, and -C genes have been relatively conserved and have become locus-specific apparently as a result of recombination and subsequent genetic drift, leading to homogenization within loci over evolutionary time. Thus, HLA class I genes have been shaped by contrasting evolutionary forces maintaining polymorphism in the exons and leading to conservation in the introns. This study provides the first extensive analysis of the introns of a highly polymorphic gene family.

Alleles↗
PubMed1997

Molecular analysis of HLA-B35 alleles and their relationship to HLA-B15 alleles.

The HLA-B35 serotype is one of the largest allelic groups of HLA class I molecules and includes four isotypes. Of the four, the B35 variant isoform is relatively rare and is the most acidic form. DNA sequencing of the rare isoforms revealed three alleles, B*1522, B*3511, and B*3517. A phylogenetic tree of HLA-B15- and HLA-B35-related alleles for the exon 2 and 3 nucleotide sequences showed that exon 2 of B*1522 clusters with B35 alleles whereas exon 3 clusters with B15 alleles. Branches of the tree suggest that the serodeterminants of B35, B62, B63, and B70 may reside in the alpha 1 domain, encoded by exon 2. The B*1520 and B*1522 genes, which type as B62 and B35, respectively, are hybrid molecules alternatively using exon 2 and exon 3 sequences of B*3501 and B*1501. A comparison of intron 2 sequences for B*3501, B*1501 and B*1522 suggests that the recombination site may have been in the region at the 3' end of intron 2. Despite being flanked by two highly polymorphic exons (exons 2 and 3), intron 2 is relatively well conserved in the B-locus, and it is characterized by seven to eight tandem repeats of the CGGGG pentanucleotide. A high degree of sequence homology and repetitive sequences are essential for a significant frequency of recombination. In this report, we reveal more about the complex evolutionary history of the HLA-B alleles.

Alleles↗
PubMed1997

Dimorphic primers derived from intron 1 for use in the molecular typing of HLA-B alleles.

We have identified a dimorphic site in intron 1 of the HLA-B gene. Oligotyping was performed on about 3000 samples using primers derived from this dimorphic site in combination with a locus-specific primer derived from intron 3. The distribution of B-alleles bearing each of the dimorphic sequences was approximately equal. These primers were mutually exclusive and yielded approximately 50% of the heterozygous samples as apparently homozygous in PCR products. Intermediate and almost high-resolution oligotyping of HLA-B alleles was achieved using 35 and 63 hybridization probes, respectively. This dimorphic site will provide a useful tool for other PCR-based HLA-B typing approaches.

Alleles↗
PubMed1996

A cDNA encoding a putative 37 kDa leucine-rich repeat (LRR) protein, p37NB, isolated from S-type neuroblastoma cell has a differential tissue distribution.

In human neuroblastoma cells in culture, three morphologically distinct types of cells are observed: neuroblastic N-type cells, Schwannian S-type cells, and intermediate I-type cells. To investigate the differences in gene expression between N-type LA1-55N and S-type LA1-5S cells of the human neuroblastoma cell line LA-N-1, we constructed a subtractive cDNA library from LA1-5S cells. One of the genes that are expressed more in S-type cells than in N-type cells was identified as previously undescribed and is the focus of this report. We cloned a full-length cDNA of this gene, p37NB, and determined its sequence. A homology search against the GenBank database showed that this was from a novel gene encoding a putative 37 kDa leucine-rich repeat (LRR) protein. Northern blot hybridization and RT-PCR showed that the p37NB gene was differentially expressed in S-type compared to N-type cells of a few neuroblastoma cell lines.

Amino Acid Sequence↗
PubMed1996

The carbohydrate moiety of the bermuda grass antigen BG60. New oligosaccharides of plant origin.

BG60 is an important allergen of Bermuda grass (Cynodon dactylon) pollen, which causes allergic responses in human. It was suggested that its carbohydrate moiety may be relevant to allergic reaction (Su, S. N., Lau, G. X., Shu, P., Yang, S. Y., Huang, S. W., and Lee, Y. C. (1996) J. Allergy Clin. Immunol., in press). Therefore, the structure of the carbohydrate moiety in BG60 was investigated. The N-linked oligosaccharides were released from the glycopeptides of BG60 by digesting with a glycoamidase from sweet almond and reductively aminated with a fluorescent reagent, 2-aminopyridine. The mixture of pyridylaminated oligosaccharides were separated by high-performance liquid chromatography (HPLC) using an octadecylsilyl (ODS) column. Five oligosaccharide fractions were isolated, and each fraction was found to be homogeneous by HPLC on an amide-silica column. The structure of each of the oligosaccharides was analyzed by the two-dimensional mapping technique (Tomiya, N., Awaya, J., Kurono, M., Endo, S., Arata, Y., and Takahashi, N. (1988) Anal. Biochem. 171, 73-90), in tandem with sequential exoglycosidase digestion. The two most abundant oligosaccharides, A and B, have an unusual structural feature, i.e. the presence of an L-Fuc alpha-(1,3)-linked to Asn-linked GlcNAc without a Xyl beta-(1,2)-linked to the branching Man (see below). To the best of our knowledge, these are the first such oligosaccharides found in plant glycoproteins.

Allergens↗
PubMed1996

Histidine-450 is the catalytic residue of L-3-hydroxyacyl coenzyme A dehydrogenase associated with the large alpha-subunit of the multienzyme complex of fatty acid oxidation from Escherichia coli.

Multienzyme complexes of fatty acid oxidation from Escherichia coli with Gln or Ala substituting for His450 or with Ala in place of Gly322 in the large alpha-subunit have been purified and characterized. The alpha/Gly322-->Ala mutation did not significantly affect the catalytic efficiencies (kcat/k(m)) of different component enzymes except for a 6.1-fold decrease in the kcat/k(m) of L-3-hydroxyacyl-CoA dehydrogenase and a 10-fold increase in the k(m) for NADH. This observation confirms the prediction [Yang, X.-Y. H., Schulz, H., Elzinga, M., & Yang, S.-Y. (1991) Biochemistry 30, 6788-6795] that the E. coli dehydrogenase has an NAD-binding site at its amino-terminal domain and structurally resembles the pig heart dehydrogenase. The pH dependence of the kcat/k(m) of the E. coli dehydrogenase suggested the catalytic involvement of an amino acid residue with a pKa of 6, which is presumably a histidine residue as proposed previously on the basis of chemical modifications. Since His450 of the E. coli multifunctional protein is the only histidine conserved in all known L-3-hydroxyacyl-CoA dehydrogenases, and since its counterpart in pig heart enzyme appeared to be close to the 3-keto group of the fatty acyl moiety of the substrate, His450 was replaced by either Gln or Ala. The catalytic properties of 3-ketoacyl-CoA thiolase, enoyl-CoA hydratase, and delta 3-cis-delta 2-trans-enoyl-CoA isomerase of the alpha/His450-->Gln mutant complex were virtually unchanged except for a small decrease in the kcat values of the latter two enzymes. In contrast, the dehydrogenase of this mutant complex was almost inactive due to a greater than 3000-fold decrease in its kcat and a 6-fold increase in the k(m) for NADH. The alpha/His450-->Ala mutant complex showed similar catalytic behaviors. Taken together, several lines of evidence lead to the conclusion that His450 is the catalytic residue of L-3-hydroxyacyl-CoA dehydrogenase of the E. coli multifunctional fatty acid oxidation protein.

3-Hydroxyacyl CoA Dehydrogenases↗
PubMed1996

Specific human cellular immunity to bcr-abl oncogene-derived peptides.

Chronic myelogenous leukemia (CML) cells are characterized by a t(9;22) translocation, which can encode one of two chimeric P210 bcr-abl fusion proteins, comprising products of either the b2a2 or the b3a2 exon junction. The junctional sequences represent potentially immunogenic tumor-specific antigens. Despite their intracellular location, the fusion proteins might be recognized immunologically by T lymphocytes if peptides, derived from these unique sequences, are capable of presentation by the major histocompatibility complex molecules. We previously found that four peptides, 9 to 11 amino acids long, spanning the b3a2 CML breakpoint bind with high or intermediate affinity to purified HLA class I molecules A3, A11, B8, or both A3 and A11. We tested the ability of these peptides to elicit specific class I restricted cytotoxic T lymphocytes (CTLs) in vitro in HLA-matched healthy donors. In addition, a longer b3a2 CML-breakpoint-derived peptide, 25 aminoacids in length (b3a2-25), was studied for its ability to induce peptide-specific, class II-mediated, T-cell proliferation. In four of four HLA-A3 donors tested, CML-A3/A11-peptide specific CTLs were induced that killed an allogeneic HLA-A3-matched peptide pulsed leukemia cell line. In two of three HLA-A3 donors, the CML-A3/A11 peptide was able to induce killing of autologous and allogeneic HLA-matched peptide-pulsed peripheral blood mononuclear cells (PBMC). CML-A3 peptide induced peptide specific CTLs in one of the four HLA A3 donors tested. No killing was observed in two HLA-B8 and two HLA-A11 donors. PBMC from seven donors were also tested for anti b3a2-25 peptide proliferation in a thymidine incorporation assay. Specific proliferation was detected in three donors, all of the HLA-DR11 haplotype. These data represent the first evidence of a cytolytic human immune response against CML bcr-abl oncogene-derived peptides and provide a rationale for developing peptide-based vaccines for this disease.

Amino Acid Sequence↗
PubMed1996

Induction of microvariant-specific CTL lines reactive to a single amino acid mismatch in bulk cultures using a transfectant expressing a single HLA class I molecule.

Alloreactivity against micromismatches in MHC class I molecules is difficult to measure. Here, we describe an in vitro model with which it is possible to examine alloreactivity against a single HLA class I allotype. The HLA class I- and class II-negative myelocytic leukemia cell line K562 was transfected with a genomic DNA clone carrying B*4403 to express a single allotype. CTL lines were generated from normal individuals carrying B*4402, B*4403, or unrelated HLA-B alleles by stimulation with B*4403- transfected K562. The bulk CTL lines generated from B*4402+ T cells against B*4403 that carry a single amino acid disparity at position 156 were specific for B*4403+ targets and did not react with targets carrying any other HLA allotype. However, the CTL lines generated from B44-negative individuals exhibited killing of the targets bearing not only B44, but also B44 CREG and a few other B alleles. Reverse transcriptase-PCR analysis of TCRs, expressed in the CTL clones uniquely specific for B*4403, showed that TCR V beta usage of alloreactive T cells directed against B*4403 was diverse but nonrandom and was affected by the HLA background of the responder. Thus, the K562-HLA transfectant system provides a useful in vitro tool to analyze alloreactivity against a single class I allele and to aid in the prediction of alloreactivity in unrelated marrow transplantation.

Alleles↗
PubMed1996

Immunologic and physicochemical studies of Bermuda grass pollen antigen BG60.

BACKGROUND: In a previous study we showed that antigen BG60 of Bermuda grass pollen contains isoallergens. Because the yield of purified isoallergens was low when a chromatofocusing technique was used, it was difficult to carry out further studies, such as determination of carbohydrate composition and structure. OBJECTIVE: The aim of this study was to establish a procedure to purify antigen BG60 proteins as a group and to characterize this group's physicochemical and immunologic properties. METHODS: A combination of chromatographic techniques (ion-exchange, gel filtration, blue gel affinity, and reverse-phase high-performance liquid chromatography) was used for the purification of BG60. Immunoblot and ELISA techniques were used to study BG60-specific IgE and IgG antibodies in patients' sera. The role of the carbohydrate moiety in antigenicity and allergenicity was examined with monoclonal antibodies and allergic sera by using periodate-treated BG60. Its carbohydrate composition was analyzed by high-performance anion-exchange chromatography with a pulsed amperometric detector. RESULTS: Homogeneity of BG60 was demonstrated by a single sharp peak in reverse-phase high-performance liquid chromatography, a single band in sodium dodecylsulfate-polyacrylamide gel electrophoresis, and only one band stained by anti-BG60 monoclonal antibody. BG60-specific IgE and IgG antibodies were shown to be present in allergic sera. Six plant lectins were found to react with BG60. On periodate treatment, BG60 reduced binding toward its monoclonal antibody and human IgE and IgG. Carbohydrate composition analysis showed that BG60 contains three kinds of sugars: mannose, N-acetylglucosamine, and fucose (in a ratio of approximately 3:2:1) and a minute amount of xylose. The carbohydrate content is approximately 7.5%, and peptide content is about 92.5%. CONCLUSION: A procedure was established for the purification of a large quantity of the BG60 antigen. The results suggest that the carbohydrate moiety of antigen BG60 may play an important role in the immune response.

Allergens↗
PubMed1996

Nucleotide sequences of MHC class I introns 1, 2, and 3 in humans and intron 2 in nonhuman primates.

HLA-class I genes are the most polymorphic genetic system yet known. The polymorphic substitutions are mostly located in exon 2 and 3, encoding alpha 1 and alpha 2 domains, respectively, which are involved in peptide binding and T cell receptor interaction. In this study, we present the sequences of the introns neighboring the polymorphic exons in humans with few examples from nonhuman primates. In general, intron sequences are found to be less polymorphic than the adjacent exons, displaying numerous locus-specific and group-specific sites. These sequences will provide important information for developing DNA based typing strategies for HLA-class I alleles.

Animals↗
PubMed1996

Allele assignment for HLA-A, -B, and -C genes to the Tenth International Histocompatibility Workshop cell lines.

Development of DNA typing for Class I HLA alleles has lagged behind that of class II for a variety of technical reasons. Following the recognition of locus specific sequences in the first and the third intron, and acquiring the ability to amplify genomic DNA by intron-based PCR primer, we have devised DNA typing of class I alleles by SSOP and direct sequencing. In this study using these techniques we provide the allelic typing of HLA-A, -B, and -C genes for the B-lymphoblastoid reference cell lines from the Tenth International Histocompatibility Workshop. We also describe some common associations of the C alleles with HLA-A and HLA-B alleles.

Alleles↗
PubMed1995

Glutamate 139 of the large alpha-subunit is the catalytic base in the dehydration of both D- and L-3-hydroxyacyl-coenzyme A but not in the isomerization of delta 3, delta 2-enoyl-coenzyme A catalyzed by the multienzyme complex of fatty acid oxidation from Escherichia coli.

Multienzyme complexes of fatty acid oxidation from Escherichia coli with either an alpha/Glu139-->Gln or an alpha/Arg134-->Gln mutation in the large alpha-subunit have been overproduced and characterized. The catalytic properties of the five different component enzymes of the alpha/Arg134-->Gln mutant complex showed no significant changes as compared with those of the wild type complex. In contrast, the 3-hydroxyacyl-coenzyme A (CoA) epimerase activity of the alpha/Glu139-->Gln mutant complex was not detected, and this mutant complex has lost almost all of the enoyl-CoA hydratase activity due to a greater than 3000-fold decrease in the kcat of the enoyl-CoA hydratase without a significant change in the Km value. The catalytic properties of 3-ketoacyl-CoA thiolase and L-3-hydroxyacyl-CoA dehydrogenase were virtually unaffected by the mutation. Together, these observations lead to the conclusion that the gamma-carboxylic group of Glu139 functions as a catalytic base in the dehydration of both D- and L-3-hydroxyacyl-CoA. These findings also support a dehydration/hydration mechanism for 3-hydroxyacyl-CoA epimerase but do not agree with an epimerase activity independent of enoyl-CoA hydratase as proposed for the glyoxysomal tetrafunctional protein [Preisig-Müller, R., Gühnemann-Schäfer, K., & Kindl, H. (1994) J. Biol. Chem. 269, 20475-20481]. Since this mutation caused the kcat of delta 3-cis-delta 2-trans-enoyl-CoA isomerase to decrease by only 60%, even though the Km value was significantly increased, it seems that Glu139 of the E. coli multifunctional protein does not function as a catalytic residue in the isomerization reaction.(ABSTRACT TRUNCATED AT 250 WORDS)

3-Hydroxyacyl CoA Dehydrogenases↗
PubMed1995

Reactivity of autologous CD4+ T lymphocytes against human melanoma. Evidence for a shared melanoma antigen presented by HLA-DR15.

Reactivity of CD8+ T lymphocytes against human melanoma has been extensively characterized, but little is known about melanoma Ags recognized by CD4+ lymphocytes. We have identified CD4+ CTL that recognize shared melanoma Ag(s) expressed by autologous melanoma cells and a subset of allogeneic melanomas. The same Ag(s) was shared by autologous and positive allogeneic melanomas by cross-blocking experiments. Cytotoxicity was directed against epitopes presented by HLA-DR on target melanoma cells, and allelic typing revealed that cytotoxicity was restricted through HLA-DR15. These CD4+ T cells released IFN-gamma, IL-4, and TNF-alpha, but not IL-2, in response to HLA-DR15+ target cells. CD4+ T cells did not lyse DR15+ nonmelanoma cell types, including melanocytes or fibroblasts (induced to express HLA-DR by IFN-gamma). Thus, by cytotoxicity assays, shared Ags were only recognized on melanoma cells but not on normal melanocytes. In summary, this analysis shows that melanoma cells share an Ag that is presented by HLA-DR15.

Antibodies, Monoclonal↗