Kinetoplastid genomics: The thin end of the wedge

Infection, Genetics and Evolution

Volumn 8, Issue 6, 2008, Pages 901-906

  Sturm, Nancy R ^a   Martinez, L L Isadora Trejo ^a   Thomas, Sean ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Bioinformatics; Leishmania; Trypanosoma; Trypanosome

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BIOINFORMATICS; FLAGELLATE; GENE SEQUENCE; GENOMICS; INTERNET; LEISHMANIA MAJOR; MEDICAL RESEARCH; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; PROTOZOAL GENETICS; SEQUENCE DATABASE; TECHNOLOGY; TRYPANOSOMA BRUCEI; TRYPANOSOMA CRUZI; WEB BROWSER;

KINETOPLASTIDA; LEISHMANIA MAJOR; TRYPANOSOMA; TRYPANOSOMA BRUCEI; TRYPANOSOMA CRUZI;

EID: 55649104309     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2008.07.001     Document Type: Note

References (68)

1. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
2. Arner E., Kindlund E., Nilsson D., Farzana F., Ferella M., Tammi M.T., and Andersson B. Database of Trypanosoma cruzi repeated genes: 20,000 additional gene variants. BMC Genomics 8 (2007) 391
3. Atwood J.A., Weatherly D.B., Minning T.A., Bundy B., Cavola C., Opperdoes F.R., Orlando R., and Tarleton R.L. The Trypanosoma cruzi proteome. Science 309 (2005) 473-476
4. Bailey T.L., Williams N., Misleh C., and Li W.W. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34 (2006) W369-373
5. Baron D.M., Ralston K.S., Kabututu Z.P., and Hill K.L. Functional genomics in Trypanosoma brucei identifies evolutionarily conserved components of motile flagella. J. Cell Sci. 120 (2007) 478-491
6. Benjamini Y., and Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. Ser. B 57 (1995) 289-300
7. Berriman M., Ghedin E., Hertz-Fowler C., Blandin G., Renauld H., Bartholomeu D.C., Lennard N.J., Caler E., Hamlin N.E., Haas B., Böhme U., Hannick L., Aslett M.A., Shallom J., Marcello L., Hou L., Wickstead B., Alsmark U.C., Arrowsmith C., Atkin R.J., Barron A.J., Bringaud F., Brooks K., Carrington M., Cherevach I., Chillingworth T.J., Churcher C., Clark L.N., Corton C.H., Cronin A., Davies R.M., Doggett J., Djikeng A., Feldblyum T., Field M.C., Fraser A., Goodhead I., Hance Z., Harper D., Harris B.R., Hauser H., Hostetler J., Ivens A., Jagels K., Johnson D., Johnson J., Jones K., Kerhornou A.X., Koo H., Larke N., Landfear S., Larkin C., Leech V., Line A., Lord A., Macleod A., Mooney P.J., Moule S., Martin D.M., Morgan G.W., Mungall K., Norbertczak H., Ormond D., Pai G., Peacock C.S., Peterson J., Quail M.A., Rabbinowitsch E., Rajandream M.A., Reitter C., Salzberg S.L., Sanders M., Schobel S., Sharp S., Simmonds M., Simpson A.J., Tallon L., Turner C.M., Tait A., Tivey A.R., Van Aken S., Walker D., Wanless D., Wang S., White B., White O., Whitehead S., Woodward J., Wortman J., Adams M.D., Embley T.M., Gull K., Ullu E., Barry J.D., Fairlamb A.H., Opperdoes F., Barrell B.G., Donelson J.E., Hall N., Fraser C.M., Melville S.E., and El-Sayed N.M. The genome of the African trypanosome Trypanosoma brucei. Science 309 (2005) 416-422
8. Bonferroni C. Teoria statistica delle classi e calcolo delle probabilita. Pubblicazioni del R Istituto Superiore di Scienze Economiche e Commerciali di Firenze 8 (1936) 3-62
9. Brenchley R., Tariq H., McElhinney H., Szö?r B., Huxley-Jones J., Stevens R., Matthews K., and Tabernero L. The TriTryp phosphatome: analysis of the protein phosphatase catalytic domains. BMC Gemonics 8 (2007) 434
10. Brobey R.K., Mei F.C., Cheng X., and Soong L. Comparative two-dimensional gel electrophoresis maps for promastigotes of Leishmania amazonensis and Leishmania major. Braz. J. Infect. Dis. 10 (2006) 1-6
11. Campbell D.A., Thomas S., and Sturm N.R. Transcription in the kinetoplastid protozoa: why be normal?. Microbes Infect. 5 (2003) 1231-1240
12. Cohen-Freue G., Holzer T.R., Forney J.D., and McMaster W.R. Global gene expression in Leishmania. Int. J. Parasitol. 37 (2007) 1077-1086
13. Colasante C., Ellis M., Ruppert T., and Voncken F. Comparative proteomics of glycosomes from bloodstream form and procyclic culture form Trypanosoma brucei brucei. Proteomics 6 (2006) 3275-3293
14. Crooks G.E., Hon G., Chandonia J.M., and Brenner S.E. WebLogo: a sequence logo generator. Genome Res. 14 (2004) 1188-1190
15. Das A., Li H., Liu T., and Bellofatto V. Biochemical characterization of Trypanosoma brucei RNA polymerase II. Mol. Biochem. Parasitol. 150 (2006) 201-210
16. De Gaudenzi J., Frasch A.C., and Clayton C. RNA-binding domain proteins in kinetoplastids: a comparative analysis. Eukaryot. Cell 4 (2005) 2106-2114
17. Dea-Ayuela M.A., Rama-Iñiguez S., and Bolás-Fernandez F. Proteomic analysis of antigens from Leishmania infantum promastigotes. Proteomics 6 (2006) 4187-4194
18. Eisen M.B., Spellman P.T., Brown P.O., and Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 14863-14868
19. El-Sayed N.M., Myler P.J., Bartholomeu D.C., Nilsson D., Aggarwal G., Tran A.N., Ghedin E., Worthey E.A., Delcher A.L., Blandin G., Westenberger S.J., Caler E., Cerqueira G.C., Branche C., Haas B., Anupama A., Arner E., Aslund L., Attipoe P., Bontempi E., Bringaud F., Burton P., Cadag E., Campbell D.A., Carrington M., Crabtree J., Darban H., da Silveira J.F., de Jong P., Edwards K., Englund P.T., Fazelina G., Feldblyum T., Ferella M., Frasch A.C., Gull K., Horn D., Hou L., Huang Y., Kindlund E., Klingbeil M., Kluge S., Koo H., Lacerda D., Levin M.J., Lorenzi H., Louie T., Machado C.R., McCulloch R., McKenna A., Mizuno Y., Mottram J.C., Nelson S., Ochaya S., Osoegawa K., Pai G., Parsons M., Pentony M., Pettersson U., Pop M., Ramirez J.L., Rinta J., Robertson L., Salzberg S.L., Sanchez D.O., Seyler A., Sharma R., Shetty J., Simpson A.J., Sisk E., Tammi M.T., Tarleton R., Teixeira S., Van Aken S., Vogt C., Ward P.N., Wickstead B., Wortman J., White O., Fraser C.M., Stuart K.D., and Andersson B. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 309 (2005) 409-415
20. El-Sayed N.M., Myler P.J., Blandin G., Berriman M., Crabtree J., Aggarwal G., Caler E., Renauld H., Worthey E.A., Hertz-Fowler C., Ghedin E., Peacock C., Bartholomeu D.C., Haas B.J., Tran A.N., Wortman J.R., Alsmark U.C., Angiuoli S., Anupama A., Badger J., Bringaud F., Cadag E., Carlton J.M., Cerqueira G.C., Creasy T., Delcher A.L., Djikeng A., Embley T.M., Hauser C., Ivens A.C., Kummerfeld S.K., Pereira-Leal J.B., Nilsson D., Peterson J., Salzberg S.L., Shallom J., Silva J.C., Sundaram J., Westenberger S., White O., Melville S.E., Donelson J.E., Andersson B., Stuart K.D., and Hall N. Comparative genomics of trypanosomatid parasitic protozoa. Science 309 (2005) 404-409
21. Feder M., Pas J., Wyrwicz L.S., and Bujnicki J.M. Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2′-O-methyltransferases. Gene 302 (2003) 129-138
22. Fernandes O., Murthy V.K., Kurath U., Degrave W.M., and Campbell D.A. Mini-exon gene variation in human pathogenic Leishmania species. Mol. Biochem. Parasitol. 66 (1994) 261-271
23. Forgber M., Basu R., Roychoudhury K., Theinert S., Roy S., Sundar S., and Walden P. Mapping the antigenicity of the parasites in Leishmania donovani infection by proteome serology. PLoS ONE 1 (2006) e40
24. Foucher A.L., Papadopoulou B., and Ouellette M. Prefractionation by digitonin extraction increases representation of the cytosolic and intracellular proteome of Leishmania infantum. J. Proteome Res. 5 (2006) 1741-1750
25. Geer L.Y., Markey S.P., Kowalak J.A., Wagner L., Xu M., Maynard D.M., Yang X., Shi W., and Bryant S.H. Open mass spectrometry search algorithm. J. Proteome Res. 3 (2004) 958-964
26. Gupta S.K., Sisodia B.S., Sinha S., Hajela K., Naik S., Shasany A.K., and Dube A. Proteomic approach for identification and characterization of novel immunostimulatory proteins from soluble antigens of Leishmania donovani promastigotes. Proteomics 7 (2007) 816-823
27. Holzer T.R., McMaster W.R., and Forney J.D. Expression profiling by whole-genome interspecies microarray hybridization reveals differential gene expression in procyclic promastigotes, lesion-derived amastigotes, and axenic amastigotes in Leishmania mexicana. Mol. Biochem. Parasitol. 146 (2006) 198-218
28. Ihaka R., and Gentleman R. R: a language for data analysis and graphics. J. Comput. Graph. Stat. 5 (1996) 299-314
29. Ivens A.C., Peacock C.S., Worthey E.A., Murphy L., Aggarwal G., Berriman M., Sisk E., Rajandream M.A., Adlem E., Aert R., Anupama A., Apostolou Z., Attipoe P., Bason N., Bauser C., Beck A., Beverley S.M., Bianchettin G., Borzym K., Bothe G., Bruschi C.V., Collins M., Cadag E., Ciarloni L., Clayton C., Coulson R.M., Cronin A., Cruz A.K., Davies R.M., De Gaudenzi J., Dobson D.E., Duesterhoeft A., Fazelina G., Fosker N., Frasch A.C., Fraser A., Fuchs M., Gabel C., Goble A., Goffeau A., Harris D., Hertz-Fowler C., Hilbert H., Horn D., Huang Y., Klages S., Knights A., Kube M., Larke N., Litvin L., Lord A., Louie T., Marra M., Masuy D., Matthews K., Michaeli S., Mottram J.C., Muller-Auer S., Munden H., Nelson S., Norbertczak H., Oliver K., O'Neil S., Pentony M., Pohl T.M., Price C., Purnelle B., Quail M.A., Rabbinowitsch E., Reinhardt R., Rieger M., Rinta J., Robben J., Robertson L., Ruiz J.C., Rutter S., Saunders D., Schafer M., Schein J., Schwartz D.C., Seeger K., Seyler A., Sharp S., Shin H., Sivam D., Squares R., Squares S., Tosato V., Vogt C., Volckaert G., Wambutt R., Warren T., Wedler H., Woodward J., Zhou S., Zimmermann W., Smith D.F., Blackwell J.M., Stuart K.D., Barrell B., et al. The genome of the kinetoplastid parasite, Leishmania major. Science 309 (2005) 436-442
30. Jackson A.P., Vaughan S., and Gull K. Comparative genomics and concerted evolution of beta-tubulin paralogs in Leishmania spp. BMC Genomics 7 (2006) 137
31. Korlach J., Marks P.J., Cicero R.L., Gray J.J., Murphy D.L., Roitman D.B., Pham T.T., Otto G.A., Foquet M., and Turner S.W. Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 1176-1181
32. Leifso K., Cohen-Freue G., Dogra N., Murray A., and McMaster W.R. Genomic and proteomic expression analysis of Leishmania promastigote and amastigote life stages: the Leishmania genome is constitutively expressed. Mol. Biochem. Parasitol. 152 (2007) 35-46
33. Liang X.H., Hury A., Hoze E., Uliel S., Myslyuk I., Apatoff A., Unger R., and Michaeli S. Genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Leishmania major indicates conservation among trypanosomatids in the repertoire and in their rRNA targets. Eukaryot. Cell 6 (2007) 361-377
34. Lukeš J., Guilbride D.L., Votypka J., Zikova A., Benne R., and Englund P.T. Kinetoplast DNA network: evolution of an improbable structure. Eukaryot. Cell 1 (2002) 495-502
35. Lukeš J., Hashimi H., and Zikova A. Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Curr. Genet. 48 (2005) 277-299
36. MacQueen J. Some methods for classification and analysis of multivariate observations. Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability (1967)
37. Maslov D.A., Westenberger S.J., Xu X., Campbell D.A., and Sturm N.R. Discovery and barcoding by analysis of spliced leader RNA gene sequences of new isolates of Trypanosomatidae from Heteroptera in Costa Rica and Ecuador. J. Eukaryot. Microbiol. 54 (2007) 57-65
38. McNicoll F., Drummelsmith J., Muller M., Madore E., Boilard N., Ouellette M., and Papadopoulou B. A combined proteomic and transcriptomic approach to the study of stage differentiation in Leishmania infantum. Proteomics 6 (2006) 3567-3581
39. Mittra B., Zamudio J.R., Bujnicki J.M., Stepinski J., Darzynkiewicz E., Campbell D.A., and Sturm N.R. The TbMTr1 spliced leader RNA cap 1 2′-O-ribose methyltransferase from Trypanosoma brucei acts with substrate specificity. J. Biol. Chem. 283 (2008) 3161-3172
40. Obado S.O., Bot C., Nilsson D., Andersson B., and Kelly J.M. Repetitive DNA is associated with centromeric domains in Trypanosoma brucei but not Trypanosoma cruzi. Genome Biol. 8 (2007) R37
41. Ochsenreiter T., Cipriano M., and Hajduk S.L. KISS: the kinetoplastid RNA editing sequence search tool. RNA 13 (2007) 1-4
42. Ochsenreiter T., Cipriano M., and Hajduk S.L. Alternative mRNA editing in trypanosomes is extensive and may contribute to mitochondrial protein diversity. PLoS ONE 3 (2008) e1566
43. Parsons M., Worthey E.A., Ward P.N., and Mottram J.C. Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi. BMC Genomics 6 (2005) 127
44. Pavlidis P., and Noble W.S. Matrix2png: a utility for visualizing matrix data. Bioinformatics 19 (2003) 295-296
45. Peacock C.S., Seeger K., Harris D., Murphy L., Ruiz J.C., Quail M.A., Peters N., Adlem E., Tivey A., Aslett M., Kerhornou A., Ivens A., Fraser A., Rajandream M.A., Carver T., Norbertczak H., Chillingworth T., Hance Z., Jagels K., Moule S., Ormond D., Rutter S., Squares R., Whitehead S., Rabbinowitsch E., Arrowsmith C., White B., Thurston S., Bringaud F., Baldauf S.L., Faulconbridge A., Jeffares D., Depledge D.P., Oyola S.O., Hilley J.D., Brito L.O., Tosi L.R., Barrell B., Cruz A.K., Mottram J.C., Smith D.F., and Berriman M. Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat. Genet. 39 (2007) 839-847
46. Pop M., and Salzberg S.L. Bioinformatics challenges of new sequencing technology. Trends Genet. 24 (2008) 142-149
47. Puechberty J., Blaineau C., Meghamla S., Crobu L., Pages M., and Bastien P. Compared genomics of the strand switch region of Leishmania chromosome 1 reveal a novel genus-specific gene and conserved structural features and sequence motifs. BMC Genomics 8 (2007) 57
48. Respuela P., Ferella M., Fada-Iglesias A., and Åslund L. Histone acetylation and methylation at sites initiating divergent polycistronic transcription in Trypanosoma cruzi. J. Biol. Chem. 283 (2008) 15884-15892
49. Salotra P., Duncan R.C., Singh R., Subba Raju B.V., Sreenivas G., and Nakhasi H.L. Upregulation of surface proteins in Leishmania donovani isolated from patients of post kala-azar dermal leishmaniasis. Microbes Infect. 8 (2006) 637-644
50. Saxena A., Lahav T., Holland N., Aggarwal G., Anupama A., Huang Y., Volpin H., Myler P.J., and Zilberstein D. Analysis of the Leishmania donovani transcriptome reveals an ordered progression of transient and permanent changes in gene expression during differentiation. Mol. Biochem. Parasitol. 152 (2007) 53-65
51. Schimanski B., Nguyen T.N., and Günzl A. Highly efficient tandem affinity purification of trypanosome protein complexes based on a novel epitope combination. Eukaryot. Cell 4 (2005) 1942-1950
52. Service R.F. Gene sequencing. The race for the $1000 genome. Science 311 (2006) 1544-1546
53. Shendure, J.A., Porreca, G.J., Church, G.M., 2008. Overview of DNA sequencing strategies. Curr. Protoc. Mol. Biol. (Chapter 7, Unit 7 1).
54. Singh N., Almeida R., Kothari H., Kumar P., Mandal G., Chatterjee M., Venkatachalam S., Govind M.K., Mandal S.K., and Sundar S. Differential gene expression analysis in antimony-unresponsive Indian kala azar (visceral leishmaniasis) clinical isolates by DNA microarray. Parasitology 134 (2007) 777-787
55. Smith D.F., Peacock C.S., and Cruz A.K. Comparative genomics: from genotype to disease phenotype in the leishmaniases. Int. J. Parasitol. 37 (2007) 1173-1186
56. Srividya G., Duncan R., Sharma P., Raju B.V., Nakhasi H.L., and Salotra P. Transcriptome analysis during the process of in vitro differentiation of Leishmania donovani using genomic microarrays. Parasitology 134 (2007) 1527-1539
57. Stuart K.D., Schnaufer A., Ernst N.L., and Panigrahi A.K. Complex management: RNA editing in trypanosomes. Trends Biochem. Sci. 30 (2005) 97-105
58. Subramaniam C., Veazey P., Redmond S., Hayes-Sinclair J., Chambers E., Carrington M., Gull K., Matthews K., Horn D., and Field M.C. Chromosome-wide analysis of gene function by RNA interference in the African trypanosome. Eukaryot. Cell 5 (2006) 1539-1549
59. Thomas S., Martinez L.L., Westenberger S.J., and Sturm N.R. A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. BMC Genomics 8 (2007) 133
60. Thomas S., Westenberger S.J., Campbell D.A., and Sturm N.R. Intragenomic spliced leader RNA array analysis of kinetoplastids reveals unexpected transcribed region diversity in Trypanosoma cruzi. Gene 352 (2005) 100-108
61. Vergnes B., Gourbal B., Girard I., Sundar S., Drummelsmith J., and Ouellette M. A proteomics screen implicates HSP83 and a small kinetoplastid calpain-related protein in drug resistance in Leishmania donovani clinical field isolates by modulating drug-induced programmed cell death. Mol. Cell. Proteomics 6 (2007) 88-101
62. Walker A., and Parkhill J. Single-cell genomics. Nat. Rev. Microbiol. 6 (2008) 176-177
63. Westenberger S.J., Barnabé C., Campbell D.A., and Sturm N.R. Two hybridization events define the population structure of Trypanosoma cruzi. Genetics 171 (2005) 527-543
64. Westenberger S.J., Cerqueira G.C., El-Sayed N.M., Zingales B., Campbell D.A., and Sturm N.R. Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and possess a conserved element in the non-coding region. BMC Genomics 7 (2006) 60
65. Westenberger S.J., Sturm N.R., Yanega D., Podlipaev S.A., Zeledón R., Campbell D.A., and Maslov D.A. Trypanosomatid biodiversity in Costa Rica: genotyping of parasites from Heteroptera using the spliced leader RNA gene. Parasitology 129 (2004) 537-547
66. Wohlschlegel J.A., Johnson E.S., Reed S.I., and Yates III J.R. Global analysis of protein sumoylation in Saccharomyces cerevisiae. J. Biol. Chem. 279 (2004) 45662-45668
67. Zamudio J.R., Mittra B., Foldynová-Trantírková S., Zeiner G.M., Lukeš J., Bujnicki J.M., Sturm N.R., and Campbell D.A. The 2′-O-ribose methyltransferase for Cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei. Mol. Cell. Biol. 27 (2007) 6084-6092
68. Zamudio J.R., Mittra B., Zeiner G.M., Feder M., Bujnicki J.M., Sturm N.R., and Campbell D.A. Complete cap 4 formation is not required for viability in Trypanosoma brucei. Eukaryot. Cell 5 (2006) 905-915