Plasmodium falciparum: the small GTPase rab11.
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Amino Acid Sequence↗
Biomedical subjects
D Chakrabarti
Publications and source records attributed to D Chakrabarti.
Detection of a functional promoter/enhancer in an intron-less human gene encoding a glutamine synthetase-like enzyme.
A human genomic clone, psi GS, containing an intron-less glutamine synthetase (GS)-encoding pseudogene, was isolated by screening a human library. A sequence of 3004 bp, containing the GS coding region and both the 5' and 3' flanking sequences, was identified that exhibits all the characteristics of a processed pseudogene. The coding region shows 93% identity with the human GS cDNA (hGS) sequence and contains two frame-shifts and two termination codons. The coding sequence is flanked by a 9-bp AT repeat and a putative polyadenylation site, AATAAA, at the 3' end. Primer extension analysis and S1 nuclease mapping showed a transcription start point (tsp) 62 bp upstream from the start codon indicating a shorter untranslated region than hGS. Transfection of HeLa cells with cat constructs containing portions of the 5' flanking sequence showed the presence of a functional promoter/enhancer within 200 bp of the tsp, independent of its orientation.
Amino Acid Sequence↗
A novel genetic interaction between daughterless and a variegating rearrangement strain of Drosophila melanogaster.
The effect of the maternal-effect mutation daughterless (da) on the reinverted In(1)BM2 strain of Drosophila melanogaster has been evaluated cytogenetically. Results show that while the variegated nature of the single X chromosome of In(1)BM2(rv) males born to female da/da x male +/+ parents is suppressed, their female sibs, homozygous for the In(1)BM2(rv) chromosome, survive the lethal effect of the absence of da+ product in their zygotes.
Animals↗
Cloning and expression of a cDNA encoding the homologue of Ran/TC4 GTP-binding protein from Plasmodium falciparum.
In our effort to identify and study proteins that are important for the progression of the malaria parasite, Plasmodium falciparum, through the cell cycle, we have cloned and sequenced the homologue of Ras-related nuclear protein Ran/TC4 (PfRan). The predicted peptide sequence of PfRan is 214 amino acids long and contains consensus motifs of the Ras superfamily. The expression of a 1.7 kb PfRan transcript changes during the cell cycle, reaching a peak at the trophozoite stage of growth of the parasite. The recombinant PfRan binds GTP similar to other Ras-like proteins.
Amino Acid Sequence↗
Analysis of expressed sequence tags from Plasmodium falciparum.
An initiative was undertaken to sequence all genes of the human malaria parasite Plasmodium falciparum in an effort to gain a better understanding at the molecular level of the parasite that inflicts much suffering in the developing world. 550 random complimentary DNA clones were partially sequenced from the intraerythrocytic form of the parasite as one of the approaches to analyze the transcribed sequences of its genome. The sequences, after editing, generated 389 expressed sequence tag sites and over 105 kb of DNA sequences. About 32% of these clones showed significant homology with other genes in the database. These clones represent 340 new Plasmodium falciparum expressed sequence tags.
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Cloning and characterization of subunit genes of ribonucleotide reductase, a cell-cycle-regulated enzyme, from Plasmodium falciparum.
Ribonucleotide reductase (EC 1.17.4.1; RNR), a cell-cycle-regulated enzyme, catalyzes the rate-limiting step in the de novo synthesis of deoxyribonucleotides by the reduction of the corresponding ribonucleotides. The important role of the RNR in DNA synthesis and cell division makes this enzyme an excellent target for chemotherapy. However, nothing is known about this enzyme from the malaria parasite Plasmodium falciparum. We have isolated cDNA clones encoding both the large and small RNR subunits. The sequences of full-length clones of the large and small RNR subunits revealed an open reading frame encoding 806 and 349 amino acids, respectively, and showed significant identity with other RNR sequences in the data base. RNA blot analysis showed that the size of the large and small RNR subunit transcripts are 5.4 kb and 2.2 kb, respectively. Both the RNR subunit transcripts fluctuate in level during the cell cycle, reaching a peak preceding maximal DNA synthesis activity. An oligodeoxynucleotide phosphorothioate that is complementary to sequences around the translational initiation codon of the small RNR subunit showed significant inhibition of growth, as measured by the inhibition in DNA synthesis.
Amino Acid Sequence↗
Gene sequence tags from Plasmodium falciparum genomic DNA fragments prepared by the "genease" activity of mung bean nuclease.
A genes-first approach to genome sequencing is described which efficiently generates gene sequence tags from genomic DNA. Mung bean nuclease (EC 3.1.30.1) cleaves the genomic DNA of many organisms before and after genes and within some introns. Analysis of gene sequence tags prepared from mung bean nuclease-digested Plasmodium falciparum DNA demonstrates that this method has several advantages over the popular cDNA expressed sequence tag approach. To date, 673 sequence tags containing over 215 kb of sequence have been generated from 400 clones. Sixty clones (15%) have significant similarity to sequences in the protein and translated nucleic acid data bases. These represent 51 unique genes, of which only 5 encode previously known P. falciparum proteins. The identified proteins include those expressed in erythrocytic, exoerythrocytic, and gametocytic stages of the parasite. Thirty percent of clones identified appear to carry complete coding regions. The spacer DNA separating genes is rarely cloned. These gene sequence tags will form a useful data base from which to initiate projects to develop new therapeutics, vaccines, and strategies to control human malaria.
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Cloning and characterization of complementary DNA encoding the eukaryotic initiation factor 2-associated 67-kDa protein (p67).
The eukaryotic initiation factor 2 (eIF-2)-associated 67-kDa glycoprotein (p67) protects eIF-2 alpha-subunit from inhibitory phosphorylation by eIF-2 kinases, such as heme-regulated inhibitor and double-stranded RNA-activated inhibitor. This promotes protein synthesis in the presence of eIF-2 kinases present in animal cells (Ray, M. K., Datta, B., Chakraborty, A., Chattopadhyay, A., Meza-Keuthen, S., and Gupta, N. K. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 539-543). In this study, the primary structure of rat p67 is determined by cDNA cloning. Based on the partial amino acid sequences of overlapping tryptic and cyanogen bromide cleaved fragments, degenerate oligonucleotides were synthesized and used as primers for the polymerase chain reaction to amplify the corresponding p67 cDNA fragment from rat liver first strand cDNA. The amplified DNA was then used as a probe to screen a rat tumor hepatoma (KRC-7) cDNA library, and a positive clone covering the entire coding region was obtained. From the cDNA sequence, an open reading frame that encodes p67 as a 480-amino acid protein with a molecular mass of 53 kilodaltons was predicted for the unglycosylated protein. The cloned cDNA was further characterized by in vitro transcription-coupled translation in micrococcal nuclease-treated reticulocyte lysate. The translated product migrated similarly to p67 in SDS-polyacrylamide gel electrophoresis and was precipitated with antibodies against p67. Northern blot analysis of rat liver poly(A)+ RNA showed a single size class (approximately 2 kilobases) of mRNA. The deduced amino acid sequence of the protein showed a highly charged N-terminal region composed of two basic polylysine blocks and an acidic aspartic acid block. The protein also exhibits significant sequence identity in the N-terminal region with human eIF-2 beta-subunit.
Amino Acid Sequence↗
Interaction of the eucaryotic peptide chain initiation factor eIF-4A with the specific elements at the 5'-untranslated sequence of human asparagine synthetase mRNA.
The resistance of certain tumor cells to the chemotherapeutic agent L-asparaginase has often been found to be associated with the presence of asparagine synthetase activity. In an attempt to study the translational regulation of the asparagine synthetase gene, the 5'-untranslated region of human asparagine synthetase cDNA was mapped by antisense oligonucleotide-mediated hybrid arrest translation in reticulocyte lysate. Three consecutive cis-acting regulatory elements, spanning from -60 to -120 bases from the initiation codon, in the 5'-untranslated region of the asparagine synthetase gene, were identified. T1 RNase footprinting analysis showed that those regulatory elements can be protected from T1 digestion when incubated with reticulocyte lysate. A 46-kDa trans-acting protein factor that interacts with the cis-acting regulatory element of asparagine synthetase mRNA was detected. This 46-kDa protein factor is most likely to be the eucaryotic peptide chain initiation factor eIF-4A as determined by immunoprecipitation experiments using a monoclonal antibody raised against reticulocyte eIF-4A.
Aspartate-Ammonia Ligase↗
Immunoregulation by processed immunoglobulin on B-cells.
According to Jerne's network hypothesis, the unique amino acid sequences of Ig variable regions, that is, the idiotypic determinants can function in immunoregulatory mechanisms and cellular interactions. Indeed, Id-specific T-cells (mostly CD4+) have since been described, but the nature of Id-positive Ig on B-cells involved in recruiting T-cells is unclear. Studies from our ongoing investigation presented here clearly show that Id can evoke both CD4+ and CD8+ T cells, and exist not only as the integral components of a bona fide antigen-binding receptor Ig but also as distinct molecular entities in processed forms on the cell surface of B-lymphocytes. Using a B-cell hybridoma, 2C3, that expresses anti-hapten (phthalate) antibody receptors on the cell surface, we induced both Id-specific CD4+ and CD8+ T effector cells. The CD4+ T cells were suppressive and mediated generation of Id-loss 2C3 variants, whereas CD8+ T cells were highly cytotoxic and selectively eliminated 2C3 cells both in vitro and in vivo. These effector cells could be induced by cell membrane-associated Ig but not by its soluble form, secreted by 2C3 cells. Antibodies to MHC class I but not class II molecules were inhibitory to this induction. Furthermore, brefeldin A (BFA), an inhibitor of MHC class I mediated processing, blocked induction of CTL but had no effect on the expression of membrane Ig. Moreover, chloroquine, an inhibitor of class II-mediated processing, had no effect. A few reports have recently appeared indicating that an exogenous Ig can be processed by B-cells in the context of MHC class II proteins.(ABSTRACT TRUNCATED AT 250 WORDS)
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Induction of syngeneic cytotoxic T lymphocytes against a B cell tumor. II. Characterization of anti-idiotypic CTL lines and clones.
In an earlier communication we showed that idiotypic immunoglobulin (Id+ Ig) of a B cell hybrid, 2C3, can induce cytotoxic T lymphocytes (CTL) in the spleens of mice that are hyperimmunized with the irradiated tumor cells. To understand the extent of heterogeneity in the splenic CTL population, stable anti-idiotypic CTL lines and clones were established from 2C3-primed splenocytes. One representative CTL line A102 which exhibited the phenotype of CD3+, CD4-, and CD8+, has been maintained in long-term culture for more than 18 months. Cytotoxic specificity of A102 was determined by cold target inhibition assay using a panel of syngeneic and allogeneic B cell tumors. The CTL line A102 was highly cytotoxic to 2C3, only weakly to other syngeneic tumors, but not at all to allogeneic B cell tumor CH12. Furthermore, CTL-mediated cytolysis was significantly abrogated by blocking 2C3 cells with anti-idiotypic monoclonal and polyclonal antibodies. These results clearly show that 2C3 Id represents the immunodominant epitope(s) recognized by the CTL line A102. To isolate a highly Id-specific effector population, A102 was repeatedly subcloned by limiting dilution. One such clone 102.F5 exhibited considerable specificity toward Id+ 2C3 while another clone 102.E10 showed no such specificity in a competitive cytotoxicity assay. This was further confirmed by the inhibition studies with anti-Id mAb. Thus, hyperimmunization with irradiated 2C3 cells evokes a spectrum of anti-2C3 cytotoxic effector cells, of which a major population is reactive to the idiotypic determinants associated with 2C3 Ig.
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Induction of syngeneic cytotoxic T lymphocytes against a B cell tumor. III. MHC class I-restricted CTL recognizes the processed form(s) of idiotype.
The purpose of this work was to determine the molecular nature of the idiotypic Ig of a B cell tumor, 2C3, involved in the induction of anti-idiotypic cytotoxic T-lymphocytes (CTL). We previously reported that hyperimmunization of mice with irradiated 2C3 cells provides effective tumor protection by inducing MHC class I-restricted CTL. Due to the enormous heterogeneity of the splenic CTL further study could not be undertaken on the idiotype (Id)-CTL interaction. Subsequently an anti-idiotypic CTL line, A102, and a highly Id-specific CTL clone, 102.F5, have been developed. In the present investigation we report that the processed forms of idiotypic determinants are responsible for induction and activation of these specific effector CTL. Inhibition studies using anti-TcR and anti-MHC class I mAbs showed that the TcR-CD3 complex of the anti-idiotypic CTL recognized 2C3 Id in the context of MHC class I antigens. The cytotoxicity of these CTL could not be inhibited with affinity-purified 2C3 Ig used as such or after pulsing with splenic antigen-presenting cells (APC). Furthermore, using brefeldin A (BFA) and chloroquine (CLQ), which are specific inhibitors of cytosolic and endosomal antigen processing pathways, respectively, it has also been observed that exposure of 2C3 to BFA but not CLQ prevents its cytolysis by both anti-idiotypic CTL line and clone. These results clearly indicate that endogenously produced idiotypic determinants of 2C3 Ig are processed in pre-Golgi vesicle, possibly in the ER, along with MHC class I antigens and then are transported to the membrane. Treatment of 2C3 with BFA, however, did not exert any effect on the expression of membrane-associated Ig of 2C3 cells. Therefore, it is the processed form rather than the bona fide receptor Ig on the cell surface that is recognized by the Id-specific CTL.
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Induction of syngeneic cytotoxic T lymphocytes against a B cell tumor. I. Role of idiotypic immunoglobulin.
In previous studies we showed that idiotypic determinants of a B cell hybrid, 2C3, was involved in the generation of idiotype (Id)-specific noncytolytic CD4+ effector T cells that suppressed the Ig expression of wild type 2C3 tumor. In the present investigation we report that Id+ Ig associated with 2C3 was also capable of eliciting syngeneic cytotoxic T lymphocytes (CTL) when mice were hyperimmunized with irradiated 2C3 cells. These effector cells were predominantly Thy 1.2+, CD8+, and CD4- and highly cytotoxic to 2C3 as shown by in vitro and in vivo assays. The unique idiotypic determinants (private Id) of 2C3 Ig was important in the induction of CTL since these effector cells were generated in mice only after immunization with Id+ 2C3 cells. In contrast, immunization of mice with 6B2, an Ig-loss variant of 2C3, and 1BF7, an unrelated syngeneic B cell hybrid which expresses Ig of the same isotype as that of 2C3 but of different Id, failed to elicit any cytotoxic response. Furthermore, incorporation of anti-idiotypic monoclonal and polyclonal antibodies into culture medium abrogated the activation of CTL during in vitro stimulation of the primed splenocytes. Induction of CTL was also inhibited by anti-MHC class I and anti-CD3 monoclonal antibodies, indicating that CD3-TcR complex of the effector T cells were involved in the recognition of Id+ Ig in the context of MHC class I antigens. These results, together with our previous observation, suggest that the anti-2C3 immune response is mediated by two kinds of effector cells, namely, CD4+ noncytolytic and CD8+ cytotoxic T cells. Moreover, the unique private Id associated with 2C3 plays a pivotal role in the induction of both of these effector cells.
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Characterization of the rDNA unit and sequence analysis of the small subunit rRNA and 5.8S rRNA genes from Tritrichomonas foetus.
The ribosomal RNA gene unit of the protozoan parasite Tritrichomonas foetus has been cloned and analyzed. Southern blot analysis of the genomic DNA showed that the ribosomal RNA gene unit is organized as a tandem head to tail repeat with a unit length of 6 kb. By Northern analysis a primary transcript of 5.8 kb was detected. Copy number analysis showed the presence of 12 copies of the ribosomal RNA gene unit. The lengths of the small subunit ribosomal RNA and 5.8S ribosomal RNA are 1571 bp and 159 bp, respectively, as determined by sequence analysis. The T. foetus small subunit ribosomal RNA sequence is one of the shortest eukaryotic small subunit rRNA sequences, similar in length to those from 2 other amitochondrial protists. Although shorter than the majority of the eukaryotic small subunit ribosomal RNAs, this sequence maintains the primary and secondary structure common to all eukaryotic small subunit ribosomal RNA structures, while truncating sequences found within the eukaryotic variable regions. The length of the large subunit ribosomal RNA was measured at 2.5 kb.
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Promotion of murine B cell differentiation by 2-mercaptoethanol in contrast to glutathione.
The role of thiol compounds in B cell proliferation and differentiation was investigated with a stable, homogeneous population of an antigen-specific plasmablastoma, 2C3. This cell line expresses both membrane and secreted forms of immunoglobulin and is arrested at an intermediate stage of B cell development. Attempts to induce its differentiation into plasma cells using antigen, anti-idiotypic antibodies, or mitogens were unsuccessful. However, cultivation of 2C3 in the presence of 2-mercaptoethanol (5 x 10(-5) M) changed its doubling time from 19.8 to 34.9 h. There was also a significant rise in intracellular glutathione and in immunoglobulin production, but little change in non-Ig protein secretion. In contrast, exposure of 2C3 to exogenous glutathione (5 x 10(-3) M) reduced the doubling time to 11.0 h, with marked increases in proliferation. Moreover, there was no significant rise in either intracellular glutathione or immunoglobulin secretion. Distinct morphological differences were also apparent at the ultrastructural level. Thus, there is a dichotomy in the action of the two thiols. Although the effects of 2-mercaptoethanol could not be reversed, the two thiols together abrogated each other's effects, implying that their actions may be mediated through a common regulatory pathway.
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Sequence microheterogeneity of the three small subunit ribosomal RNA genes of Babesia bigemina: expression in erythrocyte culture.
Three distinct ribosomal RNA (rRNA) transcription units (rDNA units), designated A, B and C, were identified in the intraerythrocytic protozoan parasite, Babesia bigemina. These rDNA units were cloned, and restriction maps were constructed showing the approximate location of the small and large rRNA coding regions. The arrangement of the genes in the genome and copy number analysis suggests the presence of a single copy of each rDNA unit per haploid genome. The complete nucleotide sequence of the small subunit rRNA coding region (1693 bp) and parts of the 5' and 3' flanking regions were determined for all three units. Units A and B have identical sequences, but unit C differs from units A and B at ten nucleotide positions, two in the small subunit rRNA coding region and four each in the adjacent 5' and 3' flanking regions. The differences in the coding region are confirmed in genomic DNA and RNA from two different isolates of B.bigemina. The RNA of both sequence types is transcribed in parasites from erythrocyte culture, however, the products of gene units A + B accumulate at a ratio of approximately 4:1 compared with the product of unit C.
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Glycosylation of eukaryotic peptide chain initiation factor 2 (eIF-2)-associated 67-kDa polypeptide (p67) and its possible role in the inhibition of eIF-2 kinase-catalyzed phosphorylation of the eIF-2 alpha-subunit.
We have reported previously that a 67-kDa polypeptide (p67) present in reticulocyte lysates protects the alpha-subunit of reticulocyte eukaryotic peptide chain initiation factor 2 (eIF-2) from phosphorylation by an eIF-2 kinase, heme-regulated protein synthesis inhibitor (Datta, B., Chakrabarti, D., Roy, A.L., and Gupta, N. K. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 3324-3328). We now present evidence that this p67 contains multiple O-linked N-acetylglucosamine (GlcNAc) residues, and these glycosyl residues may be required for p67 activity to protect the eIF-2 alpha-subunit from eIF-2 kinase phosphorylation. Our results are as follows. 1) p67 binds specifically to wheat germ agglutinin, and such binding is completely inhibited in the presence of 0.2 M GlcNAc. 2) The binding of p67 to wheat germ agglutinin leads to complete loss of p67 activity to protect the eIF-2 alpha-subunit from eIF-2 kinase phosphorylation. 3) p67 accepts 10-12 [3H]galactose molecules from UDP-[3H]galactose in the presence of galactosyltransferase. This radioactivity is resistant to endo-beta-N-acetylglucosamine F (+ peptide:N-glycosidase F) treatment but is completely lost when the 3H-labeled p67 is treated with sodium borohydride in mild alkali (beta-elimination reaction). These results suggest that p67 contains terminal GlcNAc moieties O-linked to the protein. 4) Upon hexosaminidase treatment, p67 reaction product migrated as a lower molecular mass (Mr approximately 65 kDa) protein in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. 5) A monoclonal antibody (D1) against p67 has been isolated. D1 apparently recognizes a specific GlcNAc-containing peptide epitope in p67 and does not react with hexosaminidase-treated p67. These results suggest that p67 activity in the cell may also be regulated post-transcriptionally by glycosylation of p67 protein.
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Natural mRNA is required for directing Met-tRNA(f) binding to 40S ribosomal subunits in animal cells: involvement of Co-eIF-2A in natural mRNA-directed initiation complex formation.
Two protein factors, eIF-2 as well as a high molecular weight protein complex from reticulocyte ribosomal high-salt wash which we term Co-eIF-2, promote Met-tRNA(f) binding to 40S ribosomes. This binding is dependent on the presence of an AUG codon or natural mRNAs [Roy et al. (1984) Biochem. Biophys. Res. Commun. 122, 1418-1425]. Co-eIF-2 contains two component activities, Co-eIF-2A and Co-eIF-2C. Previously, we have purified an 80-kDa polypeptide containing Co-eIF-2A activity and showed that this polypeptide is a component of Co-eIF-2 and is responsible for Co-eIF-2A activity in Co-eIF-2 [Chakravarty et al. (1985) J. Biol. Chem. 260, 6945-6949]. We now report purification of a protein complex (subunits of Mr 180K, 110K, 65K, 63K, 53K, 50K, 43K, and 40K) containing Co-eIF-2C activity and devoid of Co-eIF-2A activity. In SDS-PAGE, the purified Co-eIF-2C preparation and an eIF-3 preparation (purified in Dr. A. Wahba's laboratory) separated into seven similar major polypeptides (Mr 110K, 65K, 63K, 53K, 50K, 43K, and 40K). The 50-kDa polypeptide in Co-eIF-2C was immunoreactive with a monoclonal antibody against eIF-4A (50 kDa). We have studied the roles of purified Co-eIF-2A and Co-eIF-2C activities in ternary and Met-tRNA(f).40S ribosome complex formation. The results are as follows: (1) At low and presumably physiological factor concentration (30 nM), eIF-2 did not form detectable levels of ternary complex. Moreover, such complex formation was totally dependent on the presence of Co-eIF-2A and/or Co-eIF-2C.(ABSTRACT TRUNCATED AT 250 WORDS)
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