Depletion of the RNA-binding Protein RBP33 Results in Increased Expression of Silenced RNA Polymerase II Transcripts in Trypanosoma Brucei

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2014 Sep 13

PMID 25215501

Citations 8

Authors

Sandra M Fernandez-Moya

Mark Carrington

Antonio M Estevez

Affiliations

Soon will be listed here.

Abstract

We have characterized the RNA-binding protein RBP33 in Trypanosoma brucei, and found that it localizes to the nucleus and is essential for viability. The subset of RNAs bound to RBP33 was determined by immunoprecipitation of ribonucleoprotein complexes followed by deep sequencing. Most RBP33-bound transcripts are predicted to be non-coding. Among these, over one-third are located close to the end of transcriptional units (TUs) or have an antisense orientation within a TU. Depletion of RBP33 resulted in an increase in the level of RNAs derived from regions that are normally silenced, such as strand-switch regions, retroposon and repeat sequences. Our work provides the first example of an RNA-binding protein involved in the regulation of gene silencing in trypanosomes.

Citing Articles

Role of the RNA-binding protein ZC3H41 in the regulation of ribosomal protein messenger RNAs in trypanosomes.

Ceballos-Perez G, Rico-Jimenez M, Gomez-Linan C, Estevez A Parasit Vectors. 2023; 16(1):118.

PMID: 37004055 PMC: 10064699. DOI: 10.1186/s13071-023-05728-x.

The RNA-binding protein RBP33 dampens non-productive transcription in trypanosomes.

Gomez-Linan C, Gomez-Diaz E, Ceballos-Perez G, Fernandez-Moya S, Estevez A Nucleic Acids Res. 2022; 50(21):12251-12265.

PMID: 36454008 PMC: 9757043. DOI: 10.1093/nar/gkac1123.

The RNA-binding protein DRBD18 ensures correct mRNA splicing and polyadenylation patterns.

Bishola Tshitenge T, Clayton C RNA. 2022; 28(9):1239-1262.

PMID: 35793904 PMC: 9380746. DOI: 10.1261/rna.079258.122.

Insights into the functions and RNA binding of ZC3H22, RBP9 and DRBD7.

Erben E, Leiss K, Liu B, Gil D, Helbig C, Clayton C Parasitology. 2021; 148(10):1186-1195.

PMID: 33536101 PMC: 8312216. DOI: 10.1017/S0031182021000123.

RNA Binding Proteins and Gene Expression Regulation in .

Romagnoli B, Holetz F, Alves L, Goldenberg S Front Cell Infect Microbiol. 2020; 10:56.

PMID: 32154189 PMC: 7045066. DOI: 10.3389/fcimb.2020.00056.

References

Letunic I, Doerks T, Bork P . SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 2011; 40(Database issue):D302-5. PMC: 3245027. DOI: 10.1093/nar/gkr931. View

Fernandez-Moya S, Garcia-Perez A, Kramer S, Carrington M, Estevez A . Alterations in DRBD3 ribonucleoprotein complexes in response to stress in Trypanosoma brucei. PLoS One. 2012; 7(11):e48870. PMC: 3493610. DOI: 10.1371/journal.pone.0048870. View

Hirumi H, Hirumi K . Continuous cultivation of Trypanosoma brucei blood stream forms in a medium containing a low concentration of serum protein without feeder cell layers. J Parasitol. 1989; 75(6):985-9. View

Zhu Y, Rowley M, Bohmdorfer G, Wierzbicki A . A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing. Mol Cell. 2012; 49(2):298-309. PMC: 3560041. DOI: 10.1016/j.molcel.2012.11.011. View

Liang X, Haritan A, Uliel S, Michaeli S . trans and cis splicing in trypanosomatids: mechanism, factors, and regulation. Eukaryot Cell. 2003; 2(5):830-40. PMC: 219355. DOI: 10.1128/EC.2.5.830-840.2003. View

Cliffe L, Kieft R, Southern T, Birkeland S, Marshall M, Sweeney K . JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes. Nucleic Acids Res. 2009; 37(5):1452-62. PMC: 2655668. DOI: 10.1093/nar/gkn1067. View

Genest P, Riet B, Dumas C, Papadopoulou B, van Luenen H, Borst P . Formation of linear inverted repeat amplicons following targeting of an essential gene in Leishmania. Nucleic Acids Res. 2005; 33(5):1699-709. PMC: 1069007. DOI: 10.1093/nar/gki304. View

Patrick K, Shi H, Kolev N, 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; 106(42):17933-8. PMC: 2764927. DOI: 10.1073/pnas.0907766106. View

Guerra-Giraldez C, Quijada L, Clayton C . Compartmentation of enzymes in a microbody, the glycosome, is essential in Trypanosoma brucei. J Cell Sci. 2002; 115(Pt 13):2651-8. DOI: 10.1242/jcs.115.13.2651. View

10.

Linding R, Russell R, Neduva V, Gibson T . GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res. 2003; 31(13):3701-8. PMC: 169197. DOI: 10.1093/nar/gkg519. View

11.

Langmead B, Trapnell C, Pop M, Salzberg S . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3):R25. PMC: 2690996. DOI: 10.1186/gb-2009-10-3-r25. View

12.

Michaeli S, Podell D, Agabian N, Ullu E . The 7SL RNA homologue of Trypanosoma brucei is closely related to mammalian 7SL RNA. Mol Biochem Parasitol. 1992; 51(1):55-64. DOI: 10.1016/0166-6851(92)90200-4. View

13.

Bringaud F, Robinson D, Barradeau S, Biteau N, Baltz D, Baltz T . Characterization and disruption of a new Trypanosoma brucei repetitive flagellum protein, using double-stranded RNA inhibition. Mol Biochem Parasitol. 2001; 111(2):283-97. DOI: 10.1016/s0166-6851(00)00319-4. View

14.

Ishida T, Kinoshita K . PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res. 2007; 35(Web Server issue):W460-4. PMC: 1933209. DOI: 10.1093/nar/gkm363. View

15.

Estevez A . The RNA-binding protein TbDRBD3 regulates the stability of a specific subset of mRNAs in trypanosomes. Nucleic Acids Res. 2008; 36(14):4573-86. PMC: 2504296. DOI: 10.1093/nar/gkn406. View

16.

Kolev N, Franklin J, Carmi S, Shi H, Michaeli S, Tschudi C . The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog. 2010; 6(9):e1001090. PMC: 2936537. DOI: 10.1371/journal.ppat.1001090. View

17.

Lowell J, Kaiser F, Janzen C, Cross G . Histone H2AZ dimerizes with a novel variant H2B and is enriched at repetitive DNA in Trypanosoma brucei. J Cell Sci. 2005; 118(Pt 24):5721-30. DOI: 10.1242/jcs.02688. View

18.

Marina D, Shankar S, Natarajan P, Finn K, Madhani H . A conserved ncRNA-binding protein recruits silencing factors to heterochromatin through an RNAi-independent mechanism. Genes Dev. 2013; 27(17):1851-6. PMC: 3778239. DOI: 10.1101/gad.226019.113. View

19.

Haile S, Cristodero M, Clayton C, Estevez A . The subcellular localisation of trypanosome RRP6 and its association with the exosome. Mol Biochem Parasitol. 2006; 151(1):52-8. DOI: 10.1016/j.molbiopara.2006.10.005. View

20.

Nakai K, Horton P . PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci. 1999; 24(1):34-6. DOI: 10.1016/s0968-0004(98)01336-x. View