RNA METABOLISM IN TRYPANOSOMES

Summary

Principal Investigator: Elisabetta Ullu
Abstract: DESCRIPTION (provided by the applicant): In the last few years the study of the biology of Trypanosoma brucei, the agent of sleeping sickness in humans and nagana in cattle, has witnessed an incredible growth due to two major advances: the completion of the T. brucei genome sequence and the discovery by our laboratory of RNA interference (RNAi). By interfacing genome information with down-regulating gene function by RNAi, it is now realistic to investigate complex cellular mechanisms using global approaches. As transcription regulation plays a minor role in T. brucei, the emphasis on regulation of gene expression is primarily on post-transcriptional regulatory mechanisms. Thus, we anticipate that the enzymes governing mRNA metabolism are essential for these parasites. This proposal focuses on aspects of RNA metabolism that are either unique to trypanosomes (cap 4 biosynthesis and function) or are novel concepts in eukaryotic biology (coupling of trans-splicing and polyadenylation and the RNAi pathway). The long-term goal of this proposal remains the characterization of molecular mechanisms involved in RNA metabolism and their relevance to trypanosome biology. In the next funding period we plan to: 1. Characterize the specific RNA methyltransferases involved in cap 4 biosynthesis and investigate whether there is a mechanistic link between cap 4 formation and polyadenylation. 2. Further our understanding of the coupling of trans-splicing and polyadenylation by using a variety of approaches, including monitoring the association of processing factors along transcribed genes in living cells. 3. Further characterize the RNAi pathway in terms of its components and how the interaction of TbAGO1 with translating ribosomes is brought about.
Funding Period: 1989-12-01 - 2009-12-31
more information: NIH RePORT

Top Publications

  1. pmc On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei
    Megan Ericson
    Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
    BMC Biol 12:14. 2014
  2. pmc The emerging world of small silencing RNAs in protozoan parasites
    Vanessa D Atayde
    Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06536, USA
    Trends Parasitol 27:321-7. 2011
  3. pmc Comparative genomics reveals two novel RNAi factors in Trypanosoma brucei and provides insight into the core machinery
    Rebecca L Barnes
    Department of Internal Medicine, Yale University, New Haven, Connecticut, USA
    PLoS Pathog 8:e1002678. 2012
  4. pmc Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei
    Christian Tschudi
    Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06536, USA
    BMC Genomics 13:427. 2012
  5. pmc The structure and repertoire of small interfering RNAs in Leishmania (Viannia) braziliensis reveal diversification in the trypanosomatid RNAi pathway
    Vanessa D Atayde
    Departments of Internal Medicine, Yale University, New Haven, CT 06536, USA
    Mol Microbiol 87:580-93. 2013
  6. pmc Developmental progression to infectivity in Trypanosoma brucei triggered by an RNA-binding protein
    Nikolay G Kolev
    Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06536, USA
    Science 338:1352-3. 2012
  7. pmc Role of the Trypanosoma brucei HEN1 family methyltransferase in small interfering RNA modification
    Huafang Shi
    Department of Internal Medicine, School of Medicine, Yale University, New Haven, Connecticut, USA
    Eukaryot Cell 13:77-86. 2014
  8. pmc The emerging role of RNA-binding proteins in the life cycle of Trypanosoma brucei
    Nikolay G Kolev
    Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
    Cell Microbiol 16:482-9. 2014
  9. pmc RNA interference in protozoan parasites: achievements and challenges
    Nikolay G Kolev
    Department of Internal Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536 0812, USA
    Eukaryot Cell 10:1156-63. 2011
  10. pmc Retention and loss of RNA interference pathways in trypanosomatid protozoans
    Lon Fye Lye
    Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Pathog 6:e1001161. 2010

Scientific Experts

  • Christian Tschudi
  • Andre Schneider
  • Elisabetta Ullu
  • Huafang Shi
  • Nikolay G Kolev
  • Vanessa D Atayde
  • George K Arhin
  • Eric Aeby
  • Kristin L Patrick
  • Rebecca L Barnes
  • Lon Fye Lye
  • Shulamit Michaeli
  • Megan Ericson
  • Nicholas Carriero
  • Joseph B Franklin
  • Stephen M Beverley
  • Katherine Owens
  • Sachin Kumar Gupta
  • Nathalie Chamond
  • Appolinaire Djikeng
  • Xue Hai Liang
  • Matthias Mann
  • Michael A Janes
  • Falk Butter
  • Timothy Notton
  • Kiantra Ramey-Butler
  • George A M Cross
  • Yaara Ziporen
  • Hasmik Yepiskoposyan
  • Avraham Hury
  • Silvane M F Murta
  • Isabel Roditi
  • Ana Carolina Vieira
  • Salvatore J Turco
  • Shai Carmi
  • Bernd Schimanski
  • Oliver Mühlemann
  • Allyson Lieberman
  • Klaus Ersfeld
  • Sotiria Palioura
  • Mascha Pusnik
  • Janine Marazzi
  • Dieter Soll
  • Paula M Luz
  • Jia Peng Ruan
  • Qing Liu
  • Hongjie Li
  • Li Liu
  • Huân Ngo
  • Shuiyuan Shen
  • Iehsus Flores Pérez

Detail Information

Publications24

  1. pmc On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei
    Megan Ericson
    Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
    BMC Biol 12:14. 2014
    ..Such information can be particularly relevant to human pathogens, such as Trypanosoma brucei, the causative agent of African trypanosomiasis, since it will provide further insight into the parasite biology and life cycle...
  2. pmc The emerging world of small silencing RNAs in protozoan parasites
    Vanessa D Atayde
    Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06536, USA
    Trends Parasitol 27:321-7. 2011
    ..In this article, we focus on the striking diversity of small silencing RNAs that have been identified in several protozoan parasites and their potential biological role...
  3. pmc Comparative genomics reveals two novel RNAi factors in Trypanosoma brucei and provides insight into the core machinery
    Rebecca L Barnes
    Department of Internal Medicine, Yale University, New Haven, Connecticut, USA
    PLoS Pathog 8:e1002678. 2012
    ..The availability of the core RNAi machinery in T. brucei provides a platform to gain mechanistic insights in this ancient eukaryote and to identify the minimal set of components required to reconstitute RNAi in RNAi-deficient parasites...
  4. pmc Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei
    Christian Tschudi
    Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06536, USA
    BMC Genomics 13:427. 2012
    ..Recent evidence from higher eukaryotes suggests that a variety of genomic sequences with the potential to produce double-stranded RNA are sources for small interfering RNAs (siRNAs)...
  5. pmc The structure and repertoire of small interfering RNAs in Leishmania (Viannia) braziliensis reveal diversification in the trypanosomatid RNAi pathway
    Vanessa D Atayde
    Departments of Internal Medicine, Yale University, New Haven, CT 06536, USA
    Mol Microbiol 87:580-93. 2013
    ..Thus, our results indicate that organism-specific diversification has occurred in the RNAi pathway during evolution of the trypanosomatid lineage...
  6. pmc Developmental progression to infectivity in Trypanosoma brucei triggered by an RNA-binding protein
    Nikolay G Kolev
    Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06536, USA
    Science 338:1352-3. 2012
    ..Thus, events leading to acquisition of infectivity in the insect vector are now accessible to laboratory investigation, providing an opening for new intervention strategies...
  7. pmc Role of the Trypanosoma brucei HEN1 family methyltransferase in small interfering RNA modification
    Huafang Shi
    Department of Internal Medicine, School of Medicine, Yale University, New Haven, Connecticut, USA
    Eukaryot Cell 13:77-86. 2014
    ..Moreover, expression of TbHEN1 in Leishmania (Viannia) panamensis did not result in siRNA 3' end methylation, further emphasizing mechanistic differences in the trypanosome and Leishmania RNAi mechanisms. ..
  8. pmc The emerging role of RNA-binding proteins in the life cycle of Trypanosoma brucei
    Nikolay G Kolev
    Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
    Cell Microbiol 16:482-9. 2014
    ..Here, we discuss recent progress in the identification of RBPs with crucial roles in different stages of the T. brucei life cycle, and in elucidating targets of RBPs. ..
  9. pmc RNA interference in protozoan parasites: achievements and challenges
    Nikolay G Kolev
    Department of Internal Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536 0812, USA
    Eukaryot Cell 10:1156-63. 2011
    ..Here we review the current status of RNAi in studies of parasitic protozoa, with special emphasis on its use as a postgenomic tool...
  10. pmc Retention and loss of RNA interference pathways in trypanosomatid protozoans
    Lon Fye Lye
    Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Pathog 6:e1001161. 2010
    ....
  11. pmc The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution
    Nikolay G Kolev
    School of Public Health, Yale University, New Haven, Connecticut, United States of America
    PLoS Pathog 6:e1001090. 2010
    ..and revealed heterogeneity in pre-mRNA processing that could potentially contribute to the survival and success of the parasite population in the insect vector and the mammalian host...
  12. pmc Small nucleolar RNA interference in Trypanosoma brucei: mechanism and utilization for elucidating the function of snoRNAs
    Sachin Kumar Gupta
    The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar Ilan University, Ramat Gan 52900 Israel
    Nucleic Acids Res 38:7236-47. 2010
    ..snoRNAi of TB11Cs2C2 resulted in defects in generating srRNA-2 and LSUβ rRNA. This is the first snoRNA described so far to engage in trypanosome-specific processing events...
  13. pmc tRNASec is transcribed by RNA polymerase II in Trypanosoma brucei but not in humans
    Eric Aeby
    Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH 3012 Bern, Switzerland
    Nucleic Acids Res 38:5833-43. 2010
    ..Moreover, intron-encoded tRNAs are present in a number of eukaryotic genomes indicating that Pol-II transcription of tRNAs may not be restricted to trypanosomatids...
  14. ncbi Repression of gene expression by the coliphage MS2 coat protein in Trypanosoma brucei
    Huafang Shi
    Department of Internal Medicine, Yale Medical School, BCMM 136D, 295 Congress Avenue, Box 9812, New Haven, CT 06536 8012, USA
    Mol Biochem Parasitol 144:119-22. 2005
  15. ncbi Analysis of spliceosomal complexes in Trypanosoma brucei and silencing of two splicing factors Prp31 and Prp43
    Xue Hai Liang
    Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
    Mol Biochem Parasitol 145:29-39. 2006
    ..We identified a 45S complex carrying pre-mRNA and all the U-snRNAs, including U1 and the SL RNA, suggesting that a single spliceosomal complex may potentially conduct both trans- and cis-splicing...
  16. pmc A protein related to the vaccinia virus cap-specific methyltransferase VP39 is involved in cap 4 modification in Trypanosoma brucei
    George K Arhin
    Department of Epidemiology and Public Health, Yale University Medical School, 295 Congress Avenue, New Haven, CT 06536 0812, USA
    RNA 12:53-62. 2006
    ..Interestingly, MT57 homologs are only found in trypanosomatid protozoa that have a cap 4 structure and in poxviruses, of which vaccinia virus is a prototype...
  17. ncbi 2'-O-methylation of position 2 of the trypanosome spliced leader cap 4 is mediated by a 48 kDa protein related to vaccinia virus VP39
    George K Arhin
    Department of Internal Medicine, Yale University Medical School, 295 Congress Avenue, New Haven, CT 06536 0812, USA
    Mol Biochem Parasitol 147:137-9. 2006
  18. pmc Functional replacement of Trypanosoma brucei Argonaute by the human slicer Argonaute2
    Huafang Shi
    Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut 06536, USA
    RNA 12:943-7. 2006
    ..This finding indicates that the basic features of the RNAi mechanism are conserved from T. brucei to man...
  19. pmc An unusual Dicer-like1 protein fuels the RNA interference pathway in Trypanosoma brucei
    Huafang Shi
    Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut 06536 0812, USA
    RNA 12:2063-72. 2006
    ..This domain organization is specific to trypanosomatids and further illustrates the variable structures of protozoan Dicer-like proteins as compared to fungal and metazoan Dicer...
  20. pmc Genomic rearrangements and transcriptional analysis of the spliced leader-associated retrotransposon in RNA interference-deficient Trypanosoma brucei
    Kristin L Patrick
    Department of Epidemiology and Public Health, Yale University Medical School, 295 Congress Avenue, New Haven, CT 06536 0812, USA
    Mol Microbiol 67:435-47. 2008
    ..We speculate that the small SLACS transcripts serve as substrates for the production of siRNAs to regulate SLACS expression...
  21. pmc The canonical pathway for selenocysteine insertion is dispensable in Trypanosomes
    Eric Aeby
    Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH 3012 Bern, Switzerland
    Proc Natl Acad Sci U S A 106:5088-92. 2009
    ..These results with T. brucei imply that eukaryotes have a single pathway of Sec-tRNA(Sec) synthesis that requires Sep-tRNA(Sec) as an intermediate...
  22. pmc Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei
    Kristin L Patrick
    Department of Epidemiology and Public Health, Yale University Medical School, 295 Congress Avenue, New Haven, CT 06536 0812, USA
    Proc Natl Acad Sci U S A 106:17933-8. 2009
    ..Our finding that dcl2KO cells are more sensitive to RNAi triggers than wild-type cells has significant implications for reverse genetic analyses in this important human pathogen...
  23. pmc RNA interference in Trypanosoma brucei: role of the n-terminal RGG domain and the polyribosome association of argonaute
    Huafang Shi
    Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut 06536 8012, USA
    J Biol Chem 284:36511-20. 2009
    ..This mechanism may represent an ancient adaptation to ensure that retroposon transcripts are efficiently destroyed, if they become associated with the translational apparatus...
  24. ncbi Downregulation of the essential Trypanosoma brucei La protein affects accumulation of elongator methionyl-tRNA
    George K Arhin
    Department of Internal Medicine, Yale University Medical School, BCMM 136D, 295 Congress Avenue, Box 9812, New Haven, CT 06536 8012, USA
    Mol Biochem Parasitol 144:104-8. 2005