101
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Ekman DR, Lorenz WW, Przybyla AE, Wolfe NL, Dean JFD. SAGE analysis of transcriptome responses in Arabidopsis roots exposed to 2,4,6-trinitrotoluene. PLANT PHYSIOLOGY 2003; 133:1397-406. [PMID: 14551330 PMCID: PMC281634 DOI: 10.1104/pp.103.028019] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2003] [Revised: 07/14/2003] [Accepted: 08/09/2003] [Indexed: 05/18/2023]
Abstract
Serial analysis of gene expression was used to profile transcript levels in Arabidopsis roots and assess their responses to 2,4,6-trinitrotoluene (TNT) exposure. SAGE libraries representing control and TNT-exposed seedling root transcripts were constructed, and each was sequenced to a depth of roughly 32,000 tags. More than 19,000 unique tags were identified overall. The second most highly induced tag (27-fold increase) represented a glutathione S-transferase. Cytochrome P450 enzymes, as well as an ABC transporter and a probable nitroreductase, were highly induced by TNT exposure. Analyses also revealed an oxidative stress response upon TNT exposure. Although some increases were anticipated in light of current models for xenobiotic metabolism in plants, evidence for unsuspected conjugation pathways was also noted. Identifying transcriptome-level responses to TNT exposure will better define the metabolic pathways plants use to detoxify this xenobiotic compound, which should help improve phytoremediation strategies directed at TNT and other nitroaromatic compounds.
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Affiliation(s)
- Drew R Ekman
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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102
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Bozdech Z, Llinás M, Pulliam BL, Wong ED, Zhu J, DeRisi JL. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003; 1:E5. [PMID: 12929205 PMCID: PMC176545 DOI: 10.1371/journal.pbio.0000005] [Citation(s) in RCA: 1170] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2003] [Accepted: 07/25/2003] [Indexed: 01/27/2023] Open
Abstract
Plasmodium falciparum is the causative agent of the most burdensome form of human malaria, affecting 200-300 million individuals per year worldwide. The recently sequenced genome of P. falciparum revealed over 5,400 genes, of which 60% encode proteins of unknown function. Insights into the biochemical function and regulation of these genes will provide the foundation for future drug and vaccine development efforts toward eradication of this disease. By analyzing the complete asexual intraerythrocytic developmental cycle (IDC) transcriptome of the HB3 strain of P. falciparum, we demonstrate that at least 60% of the genome is transcriptionally active during this stage. Our data demonstrate that this parasite has evolved an extremely specialized mode of transcriptional regulation that produces a continuous cascade of gene expression, beginning with genes corresponding to general cellular processes, such as protein synthesis, and ending with Plasmodium-specific functionalities, such as genes involved in erythrocyte invasion. The data reveal that genes contiguous along the chromosomes are rarely coregulated, while transcription from the plastid genome is highly coregulated and likely polycistronic. Comparative genomic hybridization between HB3 and the reference genome strain (3D7) was used to distinguish between genes not expressed during the IDC and genes not detected because of possible sequence variations. Genomic differences between these strains were found almost exclusively in the highly antigenic subtelomeric regions of chromosomes. The simple cascade of gene regulation that directs the asexual development of P. falciparum is unprecedented in eukaryotic biology. The transcriptome of the IDC resembles a "just-in-time" manufacturing process whereby induction of any given gene occurs once per cycle and only at a time when it is required. These data provide to our knowledge the first comprehensive view of the timing of transcription throughout the intraerythrocytic development of P. falciparum and provide a resource for the identification of new chemotherapeutic and vaccine candidates.
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Affiliation(s)
- Zbynek Bozdech
- 1Department of Biochemistry and Biophysics, University of California, San FranciscoSan Francisco, CaliforniaUnited States of America
| | - Manuel Llinás
- 1Department of Biochemistry and Biophysics, University of California, San FranciscoSan Francisco, CaliforniaUnited States of America
| | - Brian Lee Pulliam
- 1Department of Biochemistry and Biophysics, University of California, San FranciscoSan Francisco, CaliforniaUnited States of America
| | - Edith D Wong
- 1Department of Biochemistry and Biophysics, University of California, San FranciscoSan Francisco, CaliforniaUnited States of America
| | - Jingchun Zhu
- 2Department of Biological and Medical Informatics, University of California, San FranciscoSan Francisco, CaliforniaUnited States of America
| | - Joseph L DeRisi
- 1Department of Biochemistry and Biophysics, University of California, San FranciscoSan Francisco, CaliforniaUnited States of America
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103
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Waller KL, Muhle RA, Ursos LM, Horrocks P, Verdier-Pinard D, Sidhu ABS, Fujioka H, Roepe PD, Fidock DA. Chloroquine resistance modulated in vitro by expression levels of the Plasmodium falciparum chloroquine resistance transporter. J Biol Chem 2003; 278:33593-601. [PMID: 12813054 DOI: 10.1074/jbc.m302215200] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasmodium falciparum malaria is increasingly difficult to treat and control due to the emergence of parasite resistance to the major antimalarials, notably chloroquine. Recent work has shown that the chloroquine resistance phenotype can be conferred by multiple amino acid mutations in the parasite digestive vacuole transmembrane protein PfCRT. Here, we have addressed whether chloroquine resistance can also be affected by changes in expression levels of this protein. Transient transfection reporter assays revealed that truncation of the pfcrt 3'-untranslated region just prior to putative polyadenylation sites resulted in a 10-fold decrease in luciferase expression levels. Using allelic exchange on a chloroquine-resistant line (7G8 from Brazil), this truncated 3'-untranslated region was inserted downstream of the pfcrt coding sequence, in the place of the endogenous 3'-untranslated region. The resulting pfcrt-modified "knockdown" clones displayed a marked decrease in pfcrt transcription and an estimated 30-40% decrease in PfCRT protein expression levels. [3H]hypoxanthine incorporation assays demonstrated up to a 40% decrease in chloroquine with or without verapamil IC50 levels of pfcrt knockdown clones, relative to the 7G8 parent. Single-cell photometric analyses were consistent with an altered intracellular pH in the knockdown clones, providing further evidence for a relationship between PfCRT, pH regulation, and chloroquine resistance. Genetic truncation of 3'-untranslated regions provides a useful approach for assessing the impact of candidate genes on drug resistance or other quantifiable phenotypes in P. falciparum.
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Affiliation(s)
- Karena L Waller
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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104
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Myrick A, Munasinghe A, Patankar S, Wirth DF. Mapping of the Plasmodium falciparum multidrug resistance gene 5'-upstream region, and evidence of induction of transcript levels by antimalarial drugs in chloroquine sensitive parasites. Mol Microbiol 2003; 49:671-83. [PMID: 12864851 DOI: 10.1046/j.1365-2958.2003.03597.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Plasmodium falciparum multidrug resistance gene, pfmdr1, has been shown to be involved in the mediation of the parasite's response to various antimalarial drugs. Previous studies of pfmdr1 expression have shown that transcript levels are increased in drug-resistant isolates. However, a detailed examination of the transcriptional regulation of this gene has not been completed. The aim of this study was to map the 5' UTR of pfmdr1, and to examine the transcriptional profile of the gene in sensitive parasites treated with four different antimalarial drugs. RT-PCR and 5'-RACE mapping showed that the 5' UTR has a length of 1.94 kb. A putative promoter has been identified via transient transfection. Northern analysis revealed a 2.1- to 2.7-fold increase in pfmdr1 expression in 3D7 parasites treated with 50 nM chloroquine for 6 h, confirming results from Serial Analysis of Gene Expression. 3D7 parasites were subsequently treated with experimentally derived IC50 concentrations of mefloquine, quinine and pyrimethamine. pfmdr1 transcript levels specifically increased 2.5-fold at 6 h in mefloquine-treated parasites and threefold in parasites treated with quinine for 30 min. There was no evidence of transcript induction in pyrimethamine-treated parasites. This is the first evidence of induction of pfmdr1 expression in sensitive cells; and suggests a novel method of transcriptional control for this gene.
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Affiliation(s)
- Alissa Myrick
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston MA, USA
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105
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Gibbings JG, Cook BP, Dufault MR, Madden SL, Khuri S, Turnbull CJ, Dunwell JM. Global transcript analysis of rice leaf and seed using SAGE technology. PLANT BIOTECHNOLOGY JOURNAL 2003; 1:271-85. [PMID: 17163904 DOI: 10.1046/j.1467-7652.2003.00026.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We have compiled two comprehensive gene expression profiles from mature leaf and immature seed tissue of rice (Oryza sativa ssp. japonica cultivar Nipponbare) using Serial Analysis of Gene Expression (SAGE) technology. Analysis revealed a total of 50 519 SAGE tags, corresponding to 15 131 unique transcripts. Of these, the large majority (approximately 70%) occur only once in both libraries. Unexpectedly, the most abundant transcript (approximately 3% of the total) in the leaf library was derived from a type 3 metallothionein gene. The overall frequency profiles of the abundant tag species from both tissues differ greatly and reveal seed tissue as exhibiting a non-typical pattern of gene expression characterized by an over abundance of a small number of transcripts coding for storage proteins. A high proportion ( approximately 80%) of the abundant tags (> or = 9) matched entries in our reference rice EST database, with many fewer matches for low abundant tags. Singleton transcripts that are common to both tissues were collated to generate a summary of low abundant transcripts that are expressed constitutively in rice tissues. Finally and most surprisingly, a significant number of tags were found to code for antisense transcripts, a finding that suggests a novel mechanism of gene regulation, and may have implications for the use of antisense constructs in transgenic technology.
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Affiliation(s)
- J George Gibbings
- BioCentre, School of Plant Sciences, The University of Reading, Reading RG6 6AS, UK
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106
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Ellis JT, Morrison DA, Reichel MP. Genomics and its impact on parasitology and the potential for development of new parasite control methods. DNA Cell Biol 2003; 22:395-403. [PMID: 12906733 DOI: 10.1089/104454903767650667] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Parasitic organisms remain the scourge of the developed and underdeveloped worlds. Malaria, schistosomiasis, leishmaniasis, and trypanosomiasis, for example, still result in a large number of human deaths each year worldwide, while drug resistance among nematodes still poses a major problem to the livestock industries. Genome projects involving parasitic organisms are now abundant, and technologies for the investigations of the parasite transcriptome and proteome are well established. There is no doubt the era of the "omics" is with parasitology, and current trends in the discipline are addressing fundamental biological questions that can make best use of the new technologies, as well as the vast amount of new data being generated. Will this become the "golden age of molecular parasitology," leading to the control of parasitic diseases that have plagued mankind for hundreds of years? The primary aim of this paper is to review advances in the general area of parasite genomics, and to outline where the application of "omics" technologies can and have impacted on the development of new control methods for parasitic organisms.
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Affiliation(s)
- John T Ellis
- Institute for the Biotechnology of Infectious Diseases, University of Technology, Sydney, Gore Hill, NSW 2065, Australia.
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107
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Ghosh A, Srinivasan P, Abraham EG, Fujioka H, Jacobs-Lorena M. Molecular strategies to study Plasmodium-mosquito interactions. Trends Parasitol 2003; 19:94-101. [PMID: 12586478 DOI: 10.1016/s1471-4922(02)00052-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is widely known that malaria kills millions of people every year. Less well recognized is the fact that the situation is steadily deteriorating for a lack of effective means to counter the disease. An essential first step towards the development of new approaches to fight malaria is a thorough understanding of the mechanisms that direct parasite growth and differentiation, including parasite-host interactions. This article reviews recent achievements and introduces some promising new technologies and approaches for studying host-parasite interactions.
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Affiliation(s)
- Anil Ghosh
- Case Western Reserve University, Department of Genetics, 10900 Euclid Avenue, Cleveland, Ohio 44106-4955, USA
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108
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Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol 2003; 4:R9. [PMID: 12620119 PMCID: PMC151308 DOI: 10.1186/gb-2003-4-2-r9] [Citation(s) in RCA: 262] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2002] [Revised: 10/10/2002] [Accepted: 12/05/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The worldwide persistence of drug-resistant Plasmodium falciparum, the most lethal variety of human malaria, is a global health concern. The P. falciparum sequencing project has brought new opportunities for identifying molecular targets for antimalarial drug and vaccine development. RESULTS We developed a software package, ArrayOligoSelector, to design an open reading frame (ORF)-specific DNA microarray using the publicly available P. falciparum genome sequence. Each gene was represented by one or more long 70 mer oligonucleotides selected on the basis of uniqueness within the genome, exclusion of low-complexity sequence, balanced base composition and proximity to the 3' end. A first-generation microarray representing approximately 6,000 ORFs of the P. falciparum genome was constructed. Array performance was evaluated through the use of control oligonucleotide sets with increasing levels of introduced mutations, as well as traditional northern blotting. Using this array, we extensively characterized the gene-expression profile of the intraerythrocytic trophozoite and schizont stages of P. falciparum. The results revealed extensive transcriptional regulation of genes specialized for processes specific to these two stages. CONCLUSIONS DNA microarrays based on long oligonucleotides are powerful tools for the functional annotation and exploration of the P. falciparum genome. Expression profiling of trophozoites and schizonts revealed genes associated with stage-specific processes and may serve as the basis for future drug targets and vaccine development.
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Affiliation(s)
- Zbynek Bozdech
- Department of Biochemistry and Biophysics, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA
| | - Jingchun Zhu
- Department of Biochemistry and Biophysics, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA
| | - Marcin P Joachimiak
- Department of Molecular and Cellular Pharmacology, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA
| | - Fred E Cohen
- Department of Molecular and Cellular Pharmacology, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA
| | - Brian Pulliam
- Department of Biochemistry and Biophysics, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA
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109
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Ganesan K, Jiang L, Rathod PK. Stochastic versus stable transcriptional differences on Plasmodium falciparum DNA microarrays. Int J Parasitol 2002; 32:1543-50. [PMID: 12435438 DOI: 10.1016/s0020-7519(02)00182-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The recent availability of the Plasmodium falciparum genome sequence has opened up convenient, large-scale analysis of transcriptional products in malaria. Protocols for cDNA labelling, cDNA hybridisation, and fluorescent signal detection developed for other organisms can be applied directly to malaria. However, P. falciparum offers unique challenges in data analysis due to stochastic variability in expression of some gene products, such as variable erythrocyte surface proteins. Careful comparison of global transcriptional patterns in two well-studied clones of P. falciparum (Dd2 and HB3) indicates that reliable, stable transcriptional alterations in malaria can be readily distinguished from stochastic processes. To do this, we utilised a complex experimental design which involves a combination of self-hybridisations and cross-hybridisations between two independently grown parasite populations for each clone being examined (for short, we call this a '2x2 CombiScan'). While even a simple 2x2 CombiScan required 12 microarray hybridisations, the effort generated output that was highly interpretable. Reliable RNA transcriptional differences between Dd2 and HB3 could be readily visualised using public algorithms for data normalisation and clustering.
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110
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Krnajski Z, Gilberger TW, Walter RD, Cowman AF, Müller S. Thioredoxin reductase is essential for the survival of Plasmodium falciparum erythrocytic stages. J Biol Chem 2002; 277:25970-5. [PMID: 12004069 DOI: 10.1074/jbc.m203539200] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human malaria parasite Plasmodium falciparum poses an increasing threat to human health in the tropical regions of the world, and the validation and assessment of possible drug targets is required for the development of new antimalarials. It has been shown that the erythrocytic stages of the parasites, which are responsible for the pathology of the disease in humans, are under enhanced oxidative stress and are particularly vulnerable to exogenous challenges by reactive oxygen species. Therefore it is postulated that the disruption of the antioxidant and/or redox systems of the parasite is a feasible way to interfere with their development during erythrocytic schizogony. In order to test this suggestion thioredoxin reductase (TrxR), an enzyme heavily involved in maintenance of redox homeostasis and antioxidant defense, was knocked out in P. falciparum. It was impossible to generate parasites with a disrupted trxR gene suggesting that TrxR is essential for P. falciparum erythrocytic stages. Technical problems were excluded by transfecting a 3' replacement construct, which recombined correctly and transfectants did not show any phenotypic alterations. In order to prove that the trxR knockout was responsible for the lethal phenotype of the null mutants, a co-transfection with both the knockout construct and a construct containing the trxR coding region under the control of the calmodulin promoter was conducted. Despite the disruption of the trxR gene, parasites were viable. In a Southern blot analysis a complicated restriction pattern was obtained, but it was shown by pulse field gel electrophoresis and field inverse gel electrophoreses that only the trxR gene locus on chromosome 9 was targeted by the constructs. It was found that the co-transfected constructs form concatemeric structures prior to integration into the trxR gene locus, which is further supported by plasmid rescue followed by restriction analyses of the plasmids. Northern and Western blot analyses proved that the co-transfectants highly overexpress TrxR from the introduced gene. Our results demonstrate that TrxR is essential for the survival of the erythrocytic stages of P. falciparum.
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Affiliation(s)
- Zita Krnajski
- Bernhard Nocht Institute for Tropical Medicine, Department of Biochemical Parasitology, 20359 Hamburg, Germany
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