Characterization of HLA-DMB polymorphism.
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Alleles↗
Biomedical subjects
M Carrington
Publications and source records attributed to M Carrington.
Haplotypic variation of the transporter associated with antigen processing (TAP) genes and their extension of HLA class II region haplotypes.
Stable cell surface presentation of HLA class I molecules requires active transport of antigenic peptides across the endoplasmic reticulum by products of two genes, TAP1 and TAP2, which map in the major histocompatibility complex class II region. Alleles of each gene are derived from a combination of variable sites at each locus. In this study, TAP1 and TAP2 alleles were identified in homozygous typing cell (HTC) lines, allowing resolution of specific haplotypes in conjunction with the highly polymorphic HLA class II region haplotypes. Three alleles at each TAP locus were found from which eight haplotypes could be assigned. Determination of TAP1 and TAP2 alleles in cell lines homozygous at DR, DQ, and DP created eight additional haplotypes beyond the number observed with these class II genes alone. Complete analysis of DR, DQ, TAP, and DP genotypes in 66 HTCs resulted in the following groups: 1) 46 homozygotes; 2) nine homozygous at DR, DQ, and TAP, but heterozygous at DP; 3) four homozygous at DR, DQ, and DP, but heterozygous at one or both TAP genes; 4) four homozygous at DR and DQ, but heterozygous at TAP and DP; and 5) three complex genotypes heterozygous at DP, TAP, and at least one of DQA1, DQB1, or DRB1 loci. TAP1 and TAP2 genes map in an area of frequent recombination. TAP alleles were determined in five DQB1, DPB1 recombinant individuals, three of which were informative. Recombination was found between DQB1 and the TAP loci in two individuals and between TAP and DPB1 in the other individual.
ATP Binding Cassette Transporter, Subfamily B, Mem↗
Characterisation of a glutamine- and proline-rich protein (QP protein) from Theileria parva.
We have isolated a clone from a Theileria parva infected lymphocyte cDNA library which has the potential to encode a protein of 480 amino acids. This protein is particularly rich in glutamine and proline and has some short repeated amino acid motifs based on the sequences QPXP and QPXQ. We have called it the 'QP protein'. Southern blotting suggests that the QP protein gene is present as a single copy in the T. parva Muguga genome. Northern blotting revealed that the gene is transcribed in both schizonts and piroplasms. We have expressed part of the QP protein as a fusion with glutathione S-transferase in Escherichia coli and used this product to raise an anti-QP protein serum. Western blots of T. parva lysates using this serum showed a major polypeptide of approximately 100 kDa and two further polypeptides of approximately 67 and 72 kDa. Indirect immunofluorescence assays using the anti-QP protein serum on infected cells showed that the protein is associated with the schizont. The pattern of staining in the indirect immunofluorescence assays and the structure of the protein suggest that it is a component of the schizont membrane.
Amino Acid Sequence↗
Culturing and biological cloning of Trypanosoma brucei.
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Animals↗
Preparation of DNA and RNA from Trypanosoma brucei.
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Animals↗
Mimicry of elastin repetitive motifs by Theileria annulata sporozoite surface antigen.
Theileria annulata is an important pathogen of cattle in the tropics. The gene sequence of a sporozoite surface antigen (SPAG-1) is reported. Data is also presented demonstrating that SPAG-1 is synthesised as a large precursor. This antigen, which is a candidate for inclusion in a subunit vaccine, shows a remarkable degree of molecular mimicry to the extracellular matrix protein elastin. It contains both repetitive motifs PGVGV and VGVAPG. Immunofluorescence using a monoclonal antibody against VGVAPG confirmed that this peptide is expressed on sporozoites as predicted. The presence of VGVAPG is particularly interesting since this is the ligand for elastin receptors on a range of cell types, including macrophages/monocytes which are a major class of host target cells. It is proposed that this antigen represents the ligand whereby T. annulata recognises its host cells.
Amino Acid Sequence↗
A method for using serum or plasma as a source of DNA for HLA typing.
A simple method for obtaining DNA from serum and plasma is described. Using appropriate primer pairs the polymorphic segments of HLA class II genes were amplified by the polymerase chain reaction (PCR) from this DNA, and typed using allele-specific oligonucleotide hybridization. When compared with DNA obtained from peripheral blood lymphocytes, the efficiency of the PCR was only minimally compromised and could be augmented by increasing the number of amplification cycles and/or by the addition of glycerol to the reaction mixture. This method serves as a reasonable alternative when no other source of DNA is available.
Base Sequence↗
The use of DNA heteroduplex patterns to map recombination within the HLA class II region.
Differential DNA heteroduplex patterns were used to investigate inheritance of HLA class II region genes in a family where a living related kidney transplant was under consideration. Serologic typing of the family members for HLA class I (HLA-A, B, and C) and class II (HLA-DR and DQ) alleles indicated that the patient (109) and one sibling (126) had inherited the same maternal and paternal HLA alleles. However, a strong reciprocal mixed lymphocyte response implied that these two individuals were not completely HLA identical. Serologic typing for HLA-DQ was confirmed by allele-specific oligonucleotide typing family members for HLA-DQ alpha and beta genes. To assess a possible nonidentical gene(s), DNA was amplified from all family members at the second exon of the DR beta, DQ alpha, DP alpha, and DP beta genes and the products were analyzed by DNA heteroduplex formation. This method showed that individuals 109 and 126 were identical at DR and DQ but differed at DP. This difference was confirmed by allele-specific oligonucleotide hybridization and indicated that 126 had inherited a recombinant maternal chromosome with a cross-over occurring in the region between the DQ beta and DP alpha genes. These data demonstrate the applicability of DNA heteroduplex patterns in establishing identity-nonidentity of alleles in the major histocompatibility complex.
Base Sequence↗
Typing of HLA-DQA1 and DQB1 using DNA single-strand conformation polymorphism.
The technique of single-strand conformation polymorphism (SSCP), which is capable of distinguishing DNA sequence variability, was adapted to the identification of the HLA-DQA1 and DQB1 alleles. Eight DQA1 alleles and 12 DQB1 alleles were distinguished by amplifying the second exon of the genes in the presence of radioactive deoxynucleotide, denaturing the products with heat, and separating the single strands by electrophoresis in nondenaturing gels. For DQA1, it was possible to distinguish the eight alleles with standard bis-acrylamide or with a Hydrolink gel matrix. Twelve DQB1 alleles were identified by a protocol employing a combination of oligohybridization and SSCP using products amplified by specific DQB1 primers.
Alleles↗
HLA phenotype is a factor in determining rate of disease progression and outcome in HIV-1-infected individuals.
HLA allele frequencies were examined for possible association(s) with the rate of disease progression and with the disease outcome (AIDS diagnosis) in a population of HIV-1-infected individuals. Certain alleles were associated with the relative rate of CD4+ T-cell decline. Association of particular alleles with several disease outcomes associated with infection was also observed. It is important to keep these two aspects (disease progression, AIDS diagnosis) separate when studying HLA in the HIV-1-infected population. Alleles that may play a role in the rate of virus speed by effecting the immune response may be different from those found to be associated with a particular disease. We feel that the only truly informative data, in this regard, can be generated from a relative precise determination of the time of infection (to study disease progression) and adequate numbers of individuals with specific diseases to study specific disease association. If such data can be generated we will have a much better understanding of the pathogenetic process(es) of HIV-1 infection.
Alleles↗
Variant specific glycoprotein of Trypanosoma brucei consists of two domains each having an independently conserved pattern of cysteine residues.
The complete amino acid sequences for nine variant specific glycoproteins (VSGs) of Trypanosoma brucei are presented. These have more than doubled the size of the VSG sequence data base and have enabled a new and more rigorous comparison to be made between amino acid sequences of different VSGs. Each VSG can be defined as a combination of an N-terminal domain type and a C-terminal domain type, based on the distribution of cysteine residues within the molecule. This identifies three N-terminal domain types and at least four C-terminal domain types. Different combinations of N and C-terminal domains can be formed; for example, in the sequences presented here, two different N-terminal domains are found in association with each of three different C-terminal domains. The biological context of the domain structure of VSGs is discussed.
Amino Acid Sequence↗
An unusual repetitive gene family in Theileria parva which is stage-specifically transcribed.
Tpr1 is a repetitive DNA element from Theileria parva which has previously been shown to be of value in strain characterisation. Further characterisation, described here, has shown that Tpr1 is present in long tandem arrays. The sequence of 8.1 kb from one end of an array has been determined. The sequence showed that Tpr1 is a 1.44-kb element which contains an ORF extending from its 5' end to the 3' end. The sequenced region contains 4 large ORFs; 2 of these consisted only of Tpr1 whilst the third consisted of Tpr1 and a 0.55-kb element (Tpr2) located 5' of Tpr1. The largest ORF consisted of Tpr1 plus Tpr2 as well as an additional 420-bp element (Tpr3) 5' of Tpr2, thus a continuous ORF arranged 5'-Tpr3-Tpr2-Tpr1-3' was formed. This ORF potentially encodes a 795 amino acid polypeptide commencing at an ATG close to the 5' end. In contrast the first in frame ATGs in the other 3 ORFs are at least 417 bp from the 5' end. Southern analysis confirmed that the sequenced region was typical of the rest of the Tpr array(s). Transcripts containing both Tpr3 and Tpr1 were detected in the piroplasm but not the schizont stages of the life cycle.
Amino Acid Sequence↗
The biology of the glycosylphosphatidylinositol-specific phospholipase C of Trypanosoma brucei.
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Amino Acid Sequence↗
2.9 A resolution structure of the N-terminal domain of a variant surface glycoprotein from Trypanosoma brucei.
The variant surface glycoprotein (VSG) of Trypanosoma brucei forms a coat on the surface of the parasite; by the expression of a series of antigenically distinct VSGs in the surface coat the parasite escapes the host immune response. The 2.9 A resolution crystal structure of the N-terminal domain of one variant, MITat 1.2, has been determined. The structure was solved using data collected from two crystal forms. Initially a partial model was built into an electron density map based on multiple isomorphous replacement phases and improved by phase combination methods. Subsequently this model was used to obtain the molecular replacement solution for a second crystal form, providing starting phases which were refined using 2-fold non-crystallographic symmetry averaging. The current model includes 362 residues and has been refined using X-PLOR to an R value of 0.22 for data between 7 and 2.9 A. The molecule is a dimer, approximately 100 A long, having an asymmetrical cross section with maximum dimensions of approximately 40 A x 60 A. Two long, approximately 70 A, alpha-helices from each monomer pack together to form, with several other helices, a core helix bundle that extends nearly the full length of the molecule. The "top" of the protein, which in the surface coat may be exposed to the external environment, is formed from the ends of the two long helices, a short three-stranded beta-sheet, and a strand having irregular conformation that packs above these secondary structure elements. Two conserved disulfide bridges are in this part of the molecule. Several elements of the MITat 1.2 sequence, which contribute to the formation of the helix bundle structure, have been identified. These elements can be found in the sequences of several different VSGs, suggesting that to some extent the VSG structure is conserved in those variants.
Amino Acid Sequence↗
Conservation of the regulatory subunit for the Clp ATP-dependent protease in prokaryotes and eukaryotes.
Bacteria, tomatoes, and trypanosomes all contain genes for a large protein with extensive homology to the regulatory subunit, ClpA, of the ATP-dependent protease of Escherichia coli, Clp. All members of the family have between 756 and 926 amino acids and contain two large regions, of 233 and 192 amino acids, each containing consensus sequences for nucleotide binding. Within these regions there is at least 85% similarity between the most distant members of the family. The high degree of similarity among the ClpA-like proteins suggests that Clp-like proteases are likely to be important participants in energy-dependent proteolysis in prokaryotic and eukaryotic cells.
ATP-Dependent Proteases↗
Duplication and transcription of procyclin genes in Trypanosoma brucei.
The genes encoding procyclin, the major glycoprotein expressed on the surface of procyclic forms of Trypanosoma brucei, comprise a multigene family. It has previously been demonstrated that procyclin genes in cloned trypanosome strains from Kenya and Uganda show restriction fragment polymorphisms. A detailed study of the Kenyan strain 227 has revealed that procyclin genes are arranged in tandem at 3 distinct loci (Pro A, B and C) and that the polymorphism is due to the duplication of 1.3 kb in the Pro A locus, which has generated an additional procyclin gene. Northern blot analysis has shown that at least 2 loci are transcribed and that a minimum of 3 procyclin genes are expressed within a cloned line. The transcription of procyclin genes is resistant to 1 mg ml-1 alpha-amanitin, whereas that of the 5' flanking gene in the Pro A locus is sensitive. This observation suggests that the two genes form part of separate transcription units with a promoter between them.
Amanitins↗
Improved characterization of Theileria parva isolates using the polymerase chain reaction and oligonucleotide probes.
Theileria parva DNA was purified from piroplasms isolated from cattle infected with 5 different East African isolates of the parasite, including the East Coast fever reference stock T. p. parva Muguga. Total cellular DNA was prepared from T. parva schizont-infected bovine lymphoblastoid cell cultures (11 isolates). Two probes, previously isolated from T. p. parva Muguga repetitive genomic DNA, were hybridized to restriction digests; closely similar restriction fragment length polymorphism (RFLP) patterns were produced, and no two isolates had the same RFLP pattern. The DNA sequences of probe PMB3, two further copies of the repeated sequence from T. p. parva Muguga, and homologous regions from T. p. parva Kiambu 4 and T. p. lawrencei 3081, were determined. Oligonucleotides were synthesized corresponding to two conserved sections flanking a region which varied between isolates. These oligonucleotides were used as primers in the polymerase chain reaction to amplify the variable region. Further oligonucleotides corresponding to sequences in this variable region were able to distinguish between isolates and no sample hybridized to both oligonucleotides. This is the first unequivocal plus/minus discrimination between groups of isolates to be achieved for T. parva.
Animals↗
Sequence and expression of the glycosyl-phosphatidylinositol-specific phospholipase C of Trypanosoma brucei.
Trypanosoma brucei contains a membrane-bound phospholipase C which converts the variant surface glycoprotein (VSG), anchored in the membrane by a C-terminal glycosyl-phosphatidylinositol moiety, into a soluble form and diacylglycerol. The amino acid sequence (358 residues) of this enzyme, derived from the nucleotide sequence of the cDNA and the gene, reveals a polypeptide which lacks an obvious N-terminal signal sequence and stretches of exclusively hydrophobic residues. These properties suggest that the phospholipase is synthesized in the cytoplasm and subsequently associates with or translocates across intracellular membranes. There are much higher levels of glycosyl-phosphatidylinositol specific phospholipase C mRNA in bloodstream form than in procyclic form trypanosomes. The phospholipase gene is probably present in one or two copies per haploid genome, probably not associated with VSG expression sites.
Amino Acid Sequence↗