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Single-target high-throughput transcription analyses reveal high levels of alternative splicing present in the FPPS/GGPPS from Plasmodium falciparum (2015)

  • Authors:
  • USP affiliated authors: PALMISANO, GIUSEPPE - ICB ; WUNDERLICH, GERHARD - ICB ; KATZIN, ALEJANDRO MIGUEL - ICB ; ALVES, JOÃO MARCELO PEREIRA - ICB
  • USP Schools: ICB; ICB; ICB; ICB
  • DOI: 10.1038/srep18429
  • Subjects: PARASITOLOGIA
  • Language: Inglês
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    Informações sobre o DOI: 10.1038/srep18429 (Fonte: oaDOI API)
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    Título do periódico: Scientific Reports

    ISSN: 2045-2322

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  • Título: Scientific Reports

    ISSN: 2045-2322

    Citescore - 2017: 4.36

    SJR - 2017: 1.533

    SNIP - 2017: 1.245


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    • ABNT

      GABRIEL, Heloisa B.; AZEVEDO, Mauro F. de; PALMISANO, Giuseppe; et al. Single-target high-throughput transcription analyses reveal high levels of alternative splicing present in the FPPS/GGPPS from Plasmodium falciparum. Scientifc Reports, London, Nature Publishing Group, v. 5, n. 184429, p. 1-13, 2015. Disponível em: < http://dx.doi.org/10.1038/srep18429 > DOI: 10.1038/srep18429.
    • APA

      Gabriel, H. B., Azevedo, M. F. de, Palmisano, G., Wunderlich, G., Kimura, E. A., Katzin, A. M., & Alves, J. M. P. (2015). Single-target high-throughput transcription analyses reveal high levels of alternative splicing present in the FPPS/GGPPS from Plasmodium falciparum. Scientifc Reports, 5( 184429), 1-13. doi:10.1038/srep18429
    • NLM

      Gabriel HB, Azevedo MF de, Palmisano G, Wunderlich G, Kimura EA, Katzin AM, Alves JMP. Single-target high-throughput transcription analyses reveal high levels of alternative splicing present in the FPPS/GGPPS from Plasmodium falciparum [Internet]. Scientifc Reports. 2015 ; 5( 184429): 1-13.Available from: http://dx.doi.org/10.1038/srep18429
    • Vancouver

      Gabriel HB, Azevedo MF de, Palmisano G, Wunderlich G, Kimura EA, Katzin AM, Alves JMP. Single-target high-throughput transcription analyses reveal high levels of alternative splicing present in the FPPS/GGPPS from Plasmodium falciparum [Internet]. Scientifc Reports. 2015 ; 5( 184429): 1-13.Available from: http://dx.doi.org/10.1038/srep18429

    Referências citadas na obra
    Singh, B. & Daneshvar, C. Human infections and detection of Plasmodium knowlesi. Clin. Microbiol. Rev. 26, 165–184 (2013).
    WHO. World Malaria Report. Report No. 978 92 4 156483 0 (World Health Organization, Switzerland, 2014).
    Snow, R. W., Guerra, C. A., Noor, A. M., Myint, H. Y. & Hay, S. I. The global distribution of clinical episodes of Plasmodium falciparum malaria. Nature 434, 214–217 (2005).
    Chakrabarti, D. et al. Protein farnesyltransferase and protein prenylation in Plasmodium falciparum. J. Biol. Chem. 277, 42066–42073 (2002).
    Borrmann, S. et al. Fosmidomycin-clindamycin for the treatment of Plasmodium falciparum malaria. J. Infect. Dis. 190, 1534–1540 (2004).
    Moura, I. C. et al. Limonene arrests parasite development and inhibits isoprenylation of proteins in Plasmodium falciparum. Antimicrob. Agents Chemother. 45, 2553–2558 (2001).
    Jomaa, H. et al. Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. Science 285, 1573–1576 (1999).
    Cassera, M. B. et al. The methylerythritol phosphate pathway is functionally active in all intraerythrocytic stages of Plasmodium falciparum. J. Biol. Chem. 279, 51749–51759 (2004).
    Flesch, G. & Rohmer, M. Prokaryotic hopanoids: the biosynthesis of the bacteriohopane skeleton. Formation of isoprenic units from two distinct acetate pools and a novel type of carbon/carbon linkage between a triterpene and D-ribose. Eur. J. Biochem. 175, 405–411 (1988).
    Eisenreich, W., Bacher, A., Arigoni, D. & Rohdich, F. Biosynthesis of isoprenoids via the non-mevalonate pathway. Cell Mol. Life Sci. 61, 1401–1426 (2004).
    Goldstein, J. L. & Brown, M. S. Regulation of the mevalonate pathway. Nature 343, 425–430 (1990).
    Tonhosolo, R. et al. Carotenoid biosynthesis in intraerythrocytic stages of Plasmodium falciparum. J. Biol. Chem. 284, 9974–9985 (2009).
    Tonhosolo, R. et al. Intraerythrocytic stages of Plasmodium falciparum biosynthesize menaquinone. FEBS Lett. 584, 4761–4768 (2010).
    Sussmann, R. A., Angeli, C. B., Peres, V. J., Kimura, E. A. & Katzin, A. M. Intraerythrocytic stages of Plasmodium falciparum biosynthesize vitamin E. FEBS Lett. 585, 3985–3991 (2011).
    Jordao, F. M. et al. Cloning and characterization of bifunctional enzyme farnesyl diphosphate/geranylgeranyl diphosphate synthase from Plasmodium falciparum. Malar. J. 12, 184 (2013).
    Wang, K. C. & Ohnuma, S. Isoprenyl diphosphate synthases. Biochim. Biophys. Acta 1529, 33–48 (2000).
    Montalvetti, A. et al. Bisphosphonates are potent inhibitors of Trypanosoma cruzi farnesyl pyrophosphate synthase. J. Biol. Chem. 276, 33930–33937 (2001).
    Montalvetti, A. et al. Farnesyl pyrophosphate synthase is an essential enzyme in Trypanosoma brucei. In vitro RNA interference and in vivo inhibition studies. J. Biol. Chem. 278, 17075–17083 (2003).
    Artz, J. D. et al. Molecular characterization of a novel geranylgeranyl pyrophosphate synthase from Plasmodium parasites. J. Biol. Chem. 286, 3315–3322 (2011).
    Ling, Y., Li, Z. H., Miranda, K., Oldfield, E. & Moreno, S. N. The farnesyl-diphosphate/geranylgeranyl-diphosphate synthase of Toxoplasma gondii is a bifunctional enzyme and a molecular target of bisphosphonates. J. Biol. Chem. 282, 30804–30816 (2007).
    Luo, S., Marchesini, N., Moreno, S. N. & Docampo, R. A plant-like vacuolar H(+)-pyrophosphatase in Plasmodium falciparum. FEBS Lett. 460, 217–220 (1999).
    Janouskovec, J., Horak, A., Obornik, M., Lukes, J. & Keeling, P. J. A common red algal origin of the apicomplexan, dinoflagellate and heterokont plastids. Proc. Natl. Acad. Sci. USA 107, 10949–10954 (2010).
    Stamm, S. et al. Function of alternative splicing. Gene 344, 1–20 (2005).
    Kelemen, O. et al. Function of alternative splicing. Gene 514, 1–30 (2013).
    Yeoh, L. M. et al. A serine-arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii. Nucleic Acids Res. 43, 4661–4675 (2015).
    Iriko, H. et al. A small-scale systematic analysis of alternative splicing in Plasmodium falciparum. Parasitol. Int. 58, 196–199 (2009).
    Gadalla, N. B. et al. Alternatively spliced transcripts and novel pseudogenes of the Plasmodium falciparum resistance-associated locus pfcrt detected in East African malaria patients. J. Antimicrob. Chemother. 70, 116–123 (2015).
    Dhar, M. K., Koul, A. & Kaul, S. Farnesyl pyrophosphate synthase: a key enzyme in isoprenoid biosynthetic pathway and potential molecular target for drug development. N. Biotechnol. 30, 114–123 (2013).
    Martin, D., Piulachs, M. D., Cunillera, N., Ferrer, A. & Belles, X. Mitochondrial targeting of farnesyl diphosphate synthase is a widespread phenomenon in eukaryotes. Biochim. Biophys. Acta 1773, 419–426 (2007).
    Lopez-Barragan, M. J. et al. Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum. BMC Genomics 12, 587 (2011).
    Otto, T. D. et al. New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol. Microbiol. 76, 12–24 (2010).
    Sorber, K., Dimon, M. T. & DeRisi, J. L. RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. Nucleic Acids Res. 39, 3820–3835 (2011).
    Bartfai, R. et al. H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3. PLoS Pathog. 6, e1001223 (2010).
    Yeh, E. & DeRisi, J. L. Chemical rescue of malaria parasites lacking an apicoplast defines organelle function in blood-stage Plasmodium falciparum. PLoS Biol. 9, e1001138 (2011).
    Waller, R. F., Reed, M. B., Cowman, A. F. & McFadden, G. I. Protein trafficking to the plastid of Plasmodium falciparum is via the secretory pathway. EMBO J. 19, 1794–1802 (2000).
    Wiesner, J. & Jomaa, H. Isoprenoid biosynthesis of the apicoplast as drug target. Curr. Drug Targets 8, 3–13 (2007).
    Ortiz-Gomez, A. et al. Farnesyl diphosphate synthase is a cytosolic enzyme in Leishmania major promastigotes and its overexpression confers resistance to risedronate. Eukaryot. Cell 5, 1057–1064 (2006).
    Ferella, M., Li, Z. H., Andersson, B. & Docampo, R. Farnesyl diphosphate synthase localizes to the cytoplasm of Trypanosoma cruzi and T. brucei. Exp. Parasitol. 119, 308–312 (2008).
    Cunillera, N., Boronat, A. & Ferrer, A. The Arabidopsis thaliana FPS1 gene generates a novel mRNA that encodes a mitochondrial farnesyl-diphosphate synthase isoform. J. Biol. Chem. 272, 15381–15388 (1997).
    Taban, A. H., Tittiger, C., Blomquist, G. J. & Welch, W. H. Isolation and characterization of farnesyl diphosphate synthase from the cotton boll weevil, Anthonomus grandis. Arch. Insect Biochem. Physiol. 71, 88–104 (2009).
    Bozdech, Z. et al. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol. 1, E5 (2003).
    Bertram, G., Innes, S., Minella, O., Richardson, J. & Stansfield, I. Endless possibilities: translation termination and stop codon recognition. Microbiology 147, 255–269 (2001).
    Jungreis, I. et al. Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Res. 21, 2096–2113 (2011).
    Blanchet, S., Cornu, D., Argentini, M. & Namy, O. New insights into the incorporation of natural suppressor tRNAs at stop codons in Saccharomyces cerevisiae. Nucleic Acids Res. 42, 10061–10072 (2014).
    Dunn, J. G., Foo, C. K., Belletier, N. G., Gavis, E. R. & Weissman, J. S. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. eLife 2, e01179 (2013).
    Gardner, M. J. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498–511 (2002).
    Lobanov, A. V. et al. The Plasmodium selenoproteome. Nucleic Acids Res. 34, 496–505 (2006).
    Mourier, T., Pain, A., Barrell, B. & Griffiths-Jones, S. A selenocysteine tRNA and SECIS element in Plasmodium falciparum. Rna 11, 119–122 (2005).
    Gamain, B. et al. Increase in glutathione peroxidase activity in malaria parasite after selenium supplementation. Free Radic. Biol. Med. 21, 559–565 (1996).
    Wang, K. & Ohnuma, S. Chain-length determination mechanism of isoprenyl diphosphate synthases and implications for molecular evolution. Trends Biochem. Sci. 24, 445–451 (1999).
    Chen, A. & Poulter, C. D. Purification and characterization of farnesyl diphosphate/geranylgeranyl diphosphate synthase. A thermostable bifunctional enzyme from Methanobacterium thermoautotrophicum. J. Biol. Chem. 268, 11002–11007 (1993).
    Narita, K., Ohnuma, S. & Nishino, T. Protein design of geranyl diphosphate synthase. Structural features that define the product specificities of prenyltransferases. J. Biochem. 126, 566–571 (1999).
    Lu, F. et al. cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome. BMC Genomics 8, 255 (2007).
    Morrissy, A. S., Griffith, M. & Marra, M. A. Extensive relationship between antisense transcription and alternative splicing in the human genome. Genome Res. 21, 1203–1212 (2011).
    Wickham, M. E., Thompson, J. K. & Cowman, A. F. Characterisation of the merozoite surface protein-2 promoter using stable and transient transfection in Plasmodium falciparum. Mol. Biochem. Parasitol. 129, 147–156 (2003).
    Fischer, K. et al. Characterization and cloning of the gene encoding the vacuolar membrane protein EXP-2 from Plasmodium falciparum. Mol. Biochem. Parasitol. 92, 47–57 (1998).
    Eshar, S. et al. A novel Plasmodium falciparum SR protein is an alternative splicing factor required for the parasites’ proliferation in human erythrocytes. Nucleic Acids Res. 40, 9903–9916 (2012).
    Trager, W. & Jensen, J. B. Human malaria parasites in continuous culture. Science 193, 673–675 (1976).
    De Azevedo, M. F. et al. Systematic analysis of FKBP inducible degradation domain tagging strategies for the human malaria parasite Plasmodium falciparum. PLoS One 7, e40981 (2012).
    Wu, Y., Sifri, C. D., Lei, H. H., Su, X. Z. & Wellems, T. E. Transfection of Plasmodium falciparum within human red blood cells. Proc. Natl. Acad. Sci. USA 92, 973–977 (1995).
    Fidock, D. A. & Wellems, T. E. Transformation with human dihydrofolate reductase renders malaria parasites insensitive to WR99210 but does not affect the intrinsic activity of proguanil. Proc. Natl. Acad. Sci. USA 94, 10931–10936 (1997).
    Furtado, G. C., Moura, I. C., Pudles, J., Alvarez, J. M. & D’Imperio Lima, M. R. Plasmodium chabaudi chabaudi: a monoclonal antibody raised against soluble antigens present in the plasma of infected mice recognizes a 250-kDa schizont glycoprotein that is secreted during schizogony. Exp. Parasitol. 91, 97–100 (1999).
    de Macedo, C. S., Uhrig, M. L., Kimura, E. A. & Katzin, A. M. Characterization of the isoprenoid chain of coenzyme Q in Plasmodium falciparum. FEMS Microbiol. Lett. 207, 13–20 (2002).
    Shestopalov, A. I., Bogachev, A. V., Murtazina, R. A., Viryasov, M. B. & Skulachev, V. P. Aeration-dependent changes in composition of the quinone pool in Escherichia coli. Evidence of post-transcriptional regulation of the quinone biosynthesis. FEBS Lett. 404, 272–274 (1997).
    Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software] v. 1.33 ( https://github.com/najoshi/sickle , 2011).
    Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
    Milne, I. et al. Tablet—next generation sequence assembly visualization. Bioinformatics 26, 401–402 (2010).
    Emanuelsson, O., Brunak, S., Von Heijne, G. & Nielsen, H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2, 953–971 (2007).
    Bullen, H. E. et al. A novel family of Apicomplexan glideosome-associated proteins with an inner membrane-anchoring role. J. Biol. Chem. 284, 25353–25363 (2009).
    Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V. & Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1, 2856–2860 (2006).
    Kall, L., Canterbury, J. D., Weston, J., Noble, W. S. & MacCoss, M. J. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 4, 923–925 (2007).