A metazoan/plant-like capping enzyme and cap modified nucleotides in the unicellular eukaryote trichomonas vaginalis

PLoS Pathogens

Volumn 6, Issue 7, 2010, Pages 1-13

  Simoes Barbosa, Augusto ^a   Hirt, Robert P ^b   Johnson, Patricia J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; NUCLEOTIDE DERIVATIVE; CAPPED RNA; GUANYLYLTRANSFERASE; NUCLEOSIDE TRIPHOSPHATASE; NUCLEOTIDE; NUCLEOTIDYLTRANSFERASE;

ARTICLE; CHEMICAL ANALYSIS; GENE LOSS; METAZOON; NONHUMAN; PHYLOGENY; PROTEIN METHYLATION; PROTEIN MODIFICATION; RNA CAPPING; TRICHOMONAS VAGINALIS; YEAST; ANIMAL; GENETICS;

EUKARYOTA; METAZOA; PROTISTA; TRICHOMONAS VAGINALIS;

ANIMALS; NUCLEOSIDE-TRIPHOSPHATASE; NUCLEOTIDES; NUCLEOTIDYLTRANSFERASES; PHYLOGENY; RNA CAPS; RNA, MESSENGER; TRICHOMONAS VAGINALIS;

EID: 77957662991     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.1000999     Document Type: Article

References (49)

1. Shuman S (2002) What messenger RNA capping tells us about eukaryotic evolution. Nat Rev Mol Cell Biol 3: 619-625.
2. Cougot N, van Dijk E, Babajko S, Seraphin B (2004) Cap-tabolism. Trends Biochem Sci 29: 436-444.
3. Varani G (1997) A cap for all occasions. Structure 5: 855-858.
4. Reddy R, Singh R, Shimba S (1992) Methylated cap structures in eukaryotic RNAs: structure, synthesis and functions. Pharmacol Ther 54: 249-267.
5. Banerjee AK (1980) 59-terminal cap structure in eucaryotic messenger ribonucleic acids. Microbiol Rev 44: 175-205.
6. Furuichi Y, Shatkin AJ (1989) Characterization of cap structures. Methods Enzymol 180: 164-176.
7. Bangs JD, Crain PF, Hashizume T, McCloskey JA, Boothroyd JC (1992) Mass spectrometry of mRNA cap 4 from trypanosomatids reveals two novel nucleosides. J Biol Chem 267: 9805-9815.
8. Mair G, Ullu E, Tschudi C (2000) Cotranscriptional cap 4 formation on the Trypanosoma brucei spliced leader RNA. J Biol Chem 275: 28994-28999.
9. Tschudi C, Ullut E (2002) Unconventional rules of small nuclear RNA transcription and cap modification in trypanosomatids. Gene Expr 10: 3-16.
10. Arhin GK, Li H, Ullu E, Tschudi C (2006) A protein related to the vaccinia virus cap-specific methyltransferase VP39 is involved in cap 4 modification in Trypanosoma brucei. RNA 12: 53-62.
11. Arhin GK, Ullu E, Tschudi C (2006) 29-O-methylation of position 2 of the trypanosome spliced leader cap 4 is mediated by a 48 kDa protein related to vaccinia virus VP39. Mol Biochem Parasitol 147: 137-139.
12. Mittra B, Zamudio JR, Bujnicki JM, Stepinski J, Darzynkiewicz E, et al. (2008) The TbMTr1 spliced leader RNA cap 1 29-O-ribose methyltransferase from Trypanosoma brucei acts with substrate specificity. J Biol Chem 283: 3161-3172.
13. Zamudio JR, Mittra B, Campbell DA, Sturm NR (2009) Hypermethylated cap 4 maximizes Trypanosoma brucei translation. Mol Microbiol 72: 1100-1110.
14. Hausmann S, Vivares CP, Shuman S (2002) Characterization of the mRNA capping apparatus of the microsporidian parasite Encephalitozoon cuniculi. J Biol Chem 277: 96-103.
15. Pei Y, Schwer B, Saiz J, Fisher RP, Shuman S (2001) RNA triphosphatase is essential in Schizosaccharomyces pombe and Candida albicans. BMC Microbiol 1: 29.
16. Ho CK, Shuman S (2001) A yeast-like mRNA capping apparatus in Plasmodium falciparum. Proc Natl Acad Sci U S A 98: 3050-3055.
17. Changela A, Ho CK, Martins A, Shuman S, Mondragon A (2001) Structure and mechanism of the RNA triphosphatase component of mammalian mRNA capping enzyme. EMBO J 20: 2575-2586.
18. Sawaya R, Shuman S (2003) Mutational analysis of the guanylyltransferase component of Mammalian mRNA capping enzyme. Biochemistry 42: 8240-8249.
19. Hausmann S, Altura MA, Witmer M, Singer SM, Elmendorf HG, et al. (2005) Yeast-like mRNA capping apparatus in Giardia lamblia. J Biol Chem 280: 12077-12086.
20. Silva E, Ullu E, Kobayashi R, Tschudi C (1998) Trypanosome capping enzymes display a novel two-domain structure. Mol Cell Biol 18: 4612-4619.
21. Ruan JP, Shen S, Ullu E, Tschudi C (2007) Evidence for a capping enzyme with specificity for the trypanosome spliced leader RNA. Mol Biochem Parasitol 156: 246-254.
22. Takagi Y, Sindkar S, Ekonomidis D, Hall MP, Ho CK (2007) Trypanosoma brucei encodes a bifunctional capping enzyme essential for cap 4 formation on the spliced leader RNA. J Biol Chem 282: 15995-16005.
23. Stiller JW (2004) Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms. Genomics Proteomics Bioinformatics 2: 70-76.
24. Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, et al. (2009) Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups". Proc Natl Acad Sci U S A 106: 3859-3864.
25. Takagi T, Moore CR, Diehn F, Buratowski S (1997) An RNA 59-triphosphatase related to the protein tyrosine phosphatases. Cell 89: 867-873.
26. Lima CD, Wang LK, Shuman S (1999) Structure and mechanism of yeast RNA triphosphatase: an essential component of the mRNA capping apparatus. Cell 99: 533-543.
27. Minge MA, Silberman JD, Orr RJ, Cavalier-Smith T, Shalchian-Tabrizi K, et al. (2009) Evolutionary position of breviate amoebae and the primary eukaryote divergence. Proc Biol Sci 276: 597-604.
28. Adl SM, Simpson AG, Farmer MA, Andersen RA, Anderson OR, et al. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 52: 399-451.
29. Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, et al. (2007) Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science 315: 207-212.
30. Simoes-Barbosa A, Meloni D, Wohlschlegel JA, Konarska MM, Johnson PJ (2008) Spliceosomal snRNAs in the unicellular eukaryote Trichomonas vaginalis are structurally conserved but lack a 59-cap structure. RNA 14: 1617-1631.
31. Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, et al. (2009) GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res 37: D526-530.
32. Wang SP, Deng L, Ho CK, Shuman S (1997) Phylogeny of mRNA capping enzymes. Proc Natl Acad Sci U S A 94: 9573-9578.
33. Shuman S (2001) Structure, mechanism, and evolution of the mRNA capping apparatus. Prog Nucleic Acid Res Mol Biol 66: 1-40.
34. Schwer B, Lehman K, Saha N, Shuman S (2001) Characterization of the mRNA capping apparatus of Candida albicans. J Biol Chem 276: 1857-1864.
35. Hausmann S, Shuman S (2005) Specificity and mechanism of RNA cap guanine-N2 methyltransferase (Tgs1). J Biol Chem 280: 4021-4024.
36. Simoes-Barbosa A, Louly C, Franco OL, Rubio MA, Alfonzo JD, et al. (2008) The divergent eukaryote Trichomonas vaginalis has an m7G cap methyltransferase capable of a single N2 methylation. Nucleic Acids Res 36: 6848-6858.
37. Liston DR, Carrero JC, Johnson PJ (1999) Upstream regulatory sequences required for expression of the Trichomonas vaginalis alpha-succinyl CoA synthetase gene. Mol Biochem Parasitol 104: 323-329.
38. Liston DR, Lau AO, Ortiz D, Smale ST, Johnson PJ (2001) Initiator recognition in a primitive eukaryote: IBP39, an initiator-binding protein from Trichomonas vaginalis. Mol Cell Biol 21: 7872-7882.
39. Roger AJ, Simpson AG (2009) Evolution: revisiting the root of the eukaryote tree. Curr Biol 19: R165-167.
40. Benarroch D, Smith P, Shuman S (2008) Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domain. Structure 16: 501-512.
41. Zheng L, Baumann U, Reymond JL (2004) An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res 32: e115.
42. Clark CG, Diamond LS (2002) Methods for cultivation of luminal parasitic protists of clinical importance. Clin Microbiol Rev 15: 329-341.
43. Grosjean H, Droogmans L, Roovers M, Keith G (2007) Detection of enzymatic activity of transfer RNA modification enzymes using radiolabeled tRNA substrates. Methods Enzymol 425: 55-101.
44. Letunic I, Doerks T, Bork P (2009) SMART 6: recent updates and new developments. Nucleic Acids Res 37: D229-232.
45. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
46. Galtier N, Gouy M, Gautier C (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12: 543-548.
47. Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105.
48. Le SQ, Gascuel O (2008) An improved general amino acid replacement matrix. Mol Biol Evol 25: 1307-1320.
49. Guindon S, Delsuc F, Dufayard JF, Gascuel O (2009) Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 537: 113-137.