Parasitic Diseases; Tropical Medicine; Trypanosomiasis, African; Genomics; RNA Interference
Public Health Interests
Parasitology; Tropical Diseases
Unraveling the biology of pathogens is fundamental toward understanding mechanisms of pathogenesis and identifying genes essential for survival in the host. Our research focuses on the protozoan parasite Trypanosoma brucei, which causes devastating diseases in humans and animals in sub-Saharan Africa. We are applying RNA interference (RNAi), namely down-regulation of gene expression by homologous double-stranded RNA, to identify genes essential for survival within the insect vector and mammalian host. In addition, high-throughput next-generation sequencing technologies (RNA-Seq) are used to analyze gene expression patterns (the transcriptome) during the developmental cycle. Lastly, we are interested in understanding gene silencing by RNAi in African trypanosomes with the objective to uncover its biological function.
Specialized Terms: African trypanosomiasis; Gene expression profiling; Gene discovery; Next-generation sequencing; RNA interference
Extensive Research Description
Professor Tschudi’s studies focus on the biology of trypanosomes the causative agents of devastating diseases in Africa and South America. Most projects in the laboratory utilize bioinformatics and modern genetic techniques to identify and dissect parasite-specific functions. The laboratory has developed several methodologies for creating mutants and has been instrumental in establishing a number of techniques to study processes at the biochemical level. These approaches will lead to a better understanding of the infectious cycle of the parasite, which involves a mammalian as well as an insect host. The long term goal is to identify candidate molecules that can be targets for chemotherapy.
Most recently, we have established and used RNA-sequencing (RNA-Seq), a novel high-throughput sequencing technology, to interrogate the transcriptome of the parasitic protozoa Trypanosoma brucei, the agent of African sleeping sickness in man and nagana in cattle.
In the course of this work, we have optimized the RNA-Seq protocol for use with trypanosomatids, built our own server, implemented a stream-lined bioinformatics pipeline and generated one of the most comprehensive genome-wide transcript maps at single-nucleotide resolution. Such information is central to the identification of functional elements, to determine the timing and regulation of gene expression in different developmental stages and to identify novel drug targets. Indeed, this work has dramatically expanded the repertoire of known genes to include over 1,000 novel genes with many displaying features suggesting that they are secreted or modulate the characteristics of membranes and thus play a role in the response of T. brucei to the changing environment during its complex life cycle. We expanded the transcriptome studies to developmental stages of T. brucei in the tsetse fly vector (in collaboration with Dr. Aksoy) and to the life cycle of Leishmania (Viannia) panamensis (in collaboration with Dr. McMahon-Pratt).
- Profiling the transcriptome of the parasitic protozoa Trypanosoma brucei, the agent of African sleeping sickness in man and nagana in cattle, by next-generation high-throughput sequencing.
- Characterization of molecular mechanisms Involved in RNA metabolism with special emphasis on RNA interference and the role of small RNAs in trypanosome biology.
- Developmental biology of African trypanosomes in its Invertebrate Host, a collaborative effort with Professor Serap Aksoy in the Department of Epidemiology of Microbial Diseases
- Characterization of enzymes involved in RNA modification, a collaboration with Professor Shulamit Michaeli at Bar Ilan University in Tel Aviv, Israel
Developmental progression to infectivity in Trypanosoma brucei triggered by an RNA-binding protein.
Kolev, N.G., Ramey-Butler, K., Cross, G.A., Ullu, E., and Tschudi, C. (2012) Science 338(6112):1352-1353.
Comparative genomics reveals two novel RNAi factors in Trypanosoma brucei and provides insight into the core machinery
Barnes, R.L., Shi, H., Kolev, N.G., Tschudi, C. and Ullu E. (2012) PLos Pathog 8(5): e1002678. doi:10.1371/journal.ppat.1002678.
The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution.
Kolev, N.G., Franklin, J.B., Carmi, S., Shi, H., Michaeli, S. and Tschudi, C. (2010). PLoS Pathog., 6(9): e1001090. doi:10.1371/journal.ppat.1001090.
Retention and loss of RNA interference pathways in trypanosomatid protozoans.
Lye, L.F., Owens, K., Shi, H., Murta, S.M., Vieira, A.C., Turco, S.J., Tschudi, C., Ullu, E. and Beverley, S.M. (2010). PLoS Pathog., 6(10): e1001161. doi:10.1371/journal.ppat.1001161.
Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei.
Patrick, K.L, Shi, H., Kolev, N.G., Ersfeld, K., Tschudi, C. and Ullu, E. (2009). Proc. Natl. Acad. Sci. U S A, 106, 17933-17938.
A protein related the vaccinia virus cap-specific methyltransferase VP39 is involved in cap 4 modification in Trypanosoma brucei.
Arhin, G.K., Li, H., Ullu, E., and Tschudi, C. (2006). RNA 12:53-62.
Transcriptome profiling of Trypanosoma brucei development in the tsetse fly vector Glossina morsitans.
Savage, A.F., Kolev, N.G., Franklin, J.B., Vigneron, A., Aksoy, S., Tschudi, C. (2016) PLoS One. e0168877. doi: 10.1371/journal.pone.0168877.
The proteome and transcriptome of the infectious metacyclic form of Trypanosoma brucei define quiescent cells primed for mammalian invasion.
Mol. Microbiol. (2017), 106, 74-92.
Full List of PubMed Publications
- Chikne V, Gupta SK, Doniger T, K SR, Cohen-Chalamish S, Waldman Ben-Asher H, Kolet L, Yahia NH, Unger R, Ullu E, Kolev NG, Tschudi C, Michaeli S: The Canonical Poly (A) Polymerase PAP1 Polyadenylates Non-Coding RNAs and Is Essential for snoRNA Biogenesis in Trypanosoma brucei. J Mol Biol. 2017 Oct 27; 2017 Apr 26. PMID: 28456523
- Christiano R, Kolev NG, Shi H, Ullu E, Walther TC, Tschudi C: The proteome and transcriptome of the infectious metacyclic form of Trypanosoma brucei define quiescent cells primed for mammalian invasion. Mol Microbiol. 2017 Oct; 2017 Aug 4. PMID: 28742275
- Kolev NG, Günzl A, Tschudi C: Metacyclic VSG expression site promoters are recognized by the same general transcription factor that is required for RNA polymerase I transcription of bloodstream expression sites. Mol Biochem Parasitol. 2017 Sep; 2017 Jul 14. PMID: 28716719
- Damasceno JD, Silva G, Tschudi C, Tosi LR: Evidence for regulated expression of Telomeric Repeat-containing RNAs (TERRA) in parasitic trypanosomatids. Mem Inst Oswaldo Cruz. 2017 Aug. PMID: 28767983
- Savage AF, Kolev NG, Franklin JB, Vigneron A, Aksoy S, Tschudi C: Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans. PLoS One. 2016; 2016 Dec 21. PMID: 28002435
- Chikne V, Doniger T, Rajan KS, Bartok O, Eliaz D, Cohen-Chalamish S, Tschudi C, Unger R, Hashem Y, Kadener S, Michaeli S: A pseudouridylation switch in rRNA is implicated in ribosome function during the life cycle of Trypanosoma brucei. Sci Rep. 2016 May 4; 2016 May 4. PMID: 27142987
- Ramey-Butler K, Ullu E, Kolev NG, Tschudi C: Synchronous expression of individual metacyclic variant surface glycoprotein genes in Trypanosoma brucei. Mol Biochem Parasitol. 2015 Mar-Apr; 2015 Apr 18. PMID: 25896436
- Kolev NG, Ullu E, Tschudi C: Construction of Trypanosoma brucei Illumina RNA-Seq libraries enriched for transcript ends. Methods Mol Biol. 2015. PMID: 25388113
- Eliaz D, Doniger T, Tkacz ID, Biswas VK, Gupta SK, Kolev NG, Unger R, Ullu E, Tschudi C, Michaeli S: Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA. RNA Biol. 2015; 2015 May 13. PMID: 25970223
- Kolev NG, Ullu E, Tschudi C: The emerging role of RNA-binding proteins in the life cycle of Trypanosoma brucei. Cell Microbiol. 2014 Apr; 2014 Feb 16. PMID: 24438230
- Ericson M, Janes MA, Butter F, Mann M, Ullu E, Tschudi C: On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei. BMC Biol. 2014 Feb 19; 2014 Feb 19. PMID: 24552149
- Shi H, Barnes RL, Carriero N, Atayde VD, Tschudi C, Ullu E: Role of the Trypanosoma brucei HEN1 family methyltransferase in small interfering RNA modification. Eukaryot Cell. 2014 Jan; 2013 Nov 1. PMID: 24186950
- Atayde VD, Shi H, Franklin JB, Carriero N, Notton T, Lye LF, Owens K, Beverley SM, Tschudi C, Ullu E: The structure and repertoire of small interfering RNAs in Leishmania (Viannia) braziliensis reveal diversification in the trypanosomatid RNAi pathway. Mol Microbiol. 2013 Feb; 2012 Dec 26. PMID: 23217017
- Kolev NG, Ramey-Butler K, Cross GA, Ullu E, Tschudi C: Developmental progression to infectivity in Trypanosoma brucei triggered by an RNA-binding protein. Science. 2012 Dec 7. PMID: 23224556
- Tschudi C, Shi H, Franklin JB, Ullu E: Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei. BMC Genomics. 2012 Aug 27; 2012 Aug 27. PMID: 22925482
- Barnes RL, Shi H, Kolev NG, Tschudi C, Ullu E: Comparative genomics reveals two novel RNAi factors in Trypanosoma brucei and provides insight into the core machinery. PLoS Pathog. 2012; 2012 May 24. PMID: 22654659
- Kolev NG, Tschudi C, Ullu E: RNA interference in protozoan parasites: achievements and challenges. Eukaryot Cell. 2011 Sep; 2011 Jul 15. PMID: 21764910
- Atayde VD, Tschudi C, Ullu E: The emerging world of small silencing RNAs in protozoan parasites. Trends Parasitol. 2011 Jul; 2011 Apr 15. PMID: 21497553
- Kolev NG, Franklin JB, Carmi S, Shi H, Michaeli S, Tschudi C: The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog. 2010 Sep 9; 2010 Sep 9. PMID: 20838601
- Shi H, Chamond N, Djikeng A, Tschudi C, Ullu E: RNA interference in Trypanosoma brucei: role of the n-terminal RGG domain and the polyribosome association of argonaute. J Biol Chem. 2009 Dec 25; 2009 Oct 30. PMID: 19880512
- Patrick KL, Shi H, Kolev NG, Ersfeld K, Tschudi C, Ullu E: Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei. Proc Natl Acad Sci U S A. 2009 Oct 20; 2009 Oct 6. PMID: 19815526
- Patrick KL, Luz PM, Ruan JP, Shi H, Ullu E, Tschudi C: Genomic rearrangements and transcriptional analysis of the spliced leader-associated retrotransposon in RNA interference-deficient Trypanosoma brucei. Mol Microbiol. 2008 Jan; 2007 Dec 5. PMID: 18067542
- Ruan JP, Shen S, Ullu E, Tschudi C: Evidence for a capping enzyme with specificity for the trypanosome spliced leader RNA. Mol Biochem Parasitol. 2007 Dec; 2007 Sep 15. PMID: 17949828
- Ruan JP, Ullu E, Tschudi C: Characterization of the Trypanosoma brucei cap hypermethylase Tgs1. Mol Biochem Parasitol. 2007 Sep; 2007 May 24. PMID: 17610965
- Shi H, Tschudi C, Ullu E: Depletion of newly synthesized Argonaute1 impairs the RNAi response in Trypanosoma brucei. RNA. 2007 Jul; 2007 May 25. PMID: 17526643
- Shi H, Tschudi C, Ullu E: An unusual Dicer-like1 protein fuels the RNA interference pathway in Trypanosoma brucei. RNA. 2006 Dec; 2006 Oct 19. PMID: 17053086
- Shi H, Tschudi C, Ullu E: Functional replacement of Trypanosoma brucei Argonaute by the human slicer Argonaute2. RNA. 2006 Jun; 2006 Apr 12. PMID: 16611939
- Arhin GK, Ullu E, Tschudi C: 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. Mol Biochem Parasitol. 2006 May; 2006 Feb 17. PMID: 16516986
- Arhin GK, Li H, Ullu E, Tschudi C: A protein related to the vaccinia virus cap-specific methyltransferase VP39 is involved in cap 4 modification in Trypanosoma brucei. RNA. 2006 Jan; 2005 Nov 21. PMID: 16301606
- Shi H, Djikeng A, Chamond N, Ngô H, Tschudi C, Ullu E: Repression of gene expression by the coliphage MS2 coat protein in Trypanosoma brucei. Mol Biochem Parasitol. 2005 Nov. PMID: 16139377
- Arhin GK, Shen S, Pérez IF, Tschudi C, Ullu E: Downregulation of the essential Trypanosoma brucei La protein affects accumulation of elongator methionyl-tRNA. Mol Biochem Parasitol. 2005 Nov. PMID: 16055205
- Ullu E, Lujan HD, Tschudi C: Small sense and antisense RNAs derived from a telomeric retroposon family in Giardia intestinalis. Eukaryot Cell. 2005 Jun. PMID: 15947207
- Li H, Tschudi C: Novel and essential subunits in the 300-kilodalton nuclear cap binding complex of Trypanosoma brucei. Mol Cell Biol. 2005 Mar. PMID: 15743819
- Shi H, Chamond N, Tschudi C, Ullu E: Selection and characterization of RNA interference-deficient trypanosomes impaired in target mRNA degradation. Eukaryot Cell. 2004 Dec. PMID: 15590819
- Shi H, Ullu E, Tschudi C: Function of the Trypanosome Argonaute 1 protein in RNA interference requires the N-terminal RGG domain and arginine 735 in the Piwi domain. J Biol Chem. 2004 Nov 26; 2004 Sep 21. PMID: 15383544
- Ruan JP, Arhin GK, Ullu E, Tschudi C: Functional characterization of a Trypanosoma brucei TATA-binding protein-related factor points to a universal regulator of transcription in trypanosomes. Mol Cell Biol. 2004 Nov. PMID: 15485927
- Arhin GK, Shen S, Irmer H, Ullu E, Tschudi C: Role of a 300-kilodalton nuclear complex in the maturation of Trypanosoma brucei initiator methionyl-tRNA. Eukaryot Cell. 2004 Aug. PMID: 15302822
- Ullu E, Tschudi C, Chakraborty T: RNA interference in protozoan parasites. Cell Microbiol. 2004 Jun. PMID: 15104593
- Narasimhan S, Montgomery RR, DePonte K, Tschudi C, Marcantonio N, Anderson JF, Sauer JR, Cappello M, Kantor FS, Fikrig E: Disruption of Ixodes scapularis anticoagulation by using RNA interference. Proc Natl Acad Sci U S A. 2004 Feb 3; 2004 Jan 26. PMID: 14745044
- Djikeng A, Shen S, Tschudi C, Ullu E: Analysis of gene function in Trypanosoma brucei using RNA interference. Methods Mol Biol. 2004. PMID: 15153635
- Arhin GK, Shen S, Ullu E, Tschudi C: A PCR-based method for gene deletion and protein tagging in Trypanosoma brucei. Methods Mol Biol. 2004. PMID: 15153634
- Djikeng A, Shen S, Tschudi C, Ullu E: Analysis of gene function in Trypanosoma brucei using RNA interference. Methods Mol Biol. 2004. PMID: 15103069
- Shi H, Djikeng A, Tschudi C, Ullu E: Argonaute protein in the early divergent eukaryote Trypanosoma brucei: control of small interfering RNA accumulation and retroposon transcript abundance. Mol Cell Biol. 2004 Jan. PMID: 14673174
- Tschudi C, Djikeng A, Shi H, Ullu E: In vivo analysis of the RNA interference mechanism in Trypanosoma brucei. Methods. 2003 Aug. PMID: 12828944
- Djikeng A, Shi H, Tschudi C, Shen S, Ullu E: An siRNA ribonucleoprotein is found associated with polyribosomes in Trypanosoma brucei. RNA. 2003 Jul. PMID: 12810914
- Shi H, Wormsley S, Tschudi C, Ullu E: Efficient transposition of preformed synaptic Tn5 complexes in Trypanosoma brucei. Mol Biochem Parasitol. 2002 Apr 30. PMID: 11985870
- Ullu E, Djikeng A, Shi H, Tschudi C: RNA interference: advances and questions. Philos Trans R Soc Lond B Biol Sci. 2002 Jan 29. PMID: 11839183
- Tschudi C, Ullut E: Unconventional rules of small nuclear RNA transcription and cap modification in trypanosomatids. Gene Expr. 2002. PMID: 11868986