Depletion of the Trypanosome Pumilio Domain Protein PUF2 or of Some Other Essential Proteins Causes Transcriptome Changes Related to Coding Region Length

Overview

Journal Eukaryot Cell

Publisher American Society for Microbiology

Specialty Molecular Biology

Date 2014 Apr 1

PMID 24681684

Citations 17

Authors

Bhaskar Anand Jha

Abeer Fadda

Clementine Merce

Elisha Mugo

Dorothea Droll

Christine Clayton

Affiliations

Soon will be listed here.

Abstract

Pumilio domain RNA-binding proteins are known mainly as posttranscriptional repressors of gene expression that reduce mRNA translation and stability. Trypanosoma brucei has 11 PUF proteins. We show here that PUF2 is in the cytosol, with roughly the same number of molecules per cell as there are mRNAs. Although PUF2 exhibits a low level of in vivo RNA binding, it is not associated with polysomes. PUF2 also decreased reporter mRNA levels in a tethering assay, consistent with a repressive role. Depletion of PUF2 inhibited growth of bloodstream-form trypanosomes, causing selective loss of mRNAs with long open reading frames and increases in mRNAs with shorter open reading frames. Reexamination of published RNASeq data revealed the same trend in cells depleted of some other proteins. We speculate that these length effects could be caused by inhibition of the elongation phase of transcription or by an influence of translation status or polysomal conformation on mRNA decay.

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References

Wang Z, Tollervey J, Briese M, Turner D, Ule J . CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo. Methods. 2009; 48(3):287-93. DOI: 10.1016/j.ymeth.2009.02.021. View

Archer S, Luu V, de Queiroz R, Brems S, Clayton C . Trypanosoma brucei PUF9 regulates mRNAs for proteins involved in replicative processes over the cell cycle. PLoS Pathog. 2009; 5(8):e1000565. PMC: 2727004. DOI: 10.1371/journal.ppat.1000565. View

Cridge A, Castelli L, Smirnova J, Selley J, Rowe W, Hubbard S . Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins. Nucleic Acids Res. 2010; 38(22):8039-50. PMC: 3001062. DOI: 10.1093/nar/gkq686. View

Kruk J, Dutta A, Fu J, Gilmour D, Reese J . The multifunctional Ccr4-Not complex directly promotes transcription elongation. Genes Dev. 2011; 25(6):581-93. PMC: 3059832. DOI: 10.1101/gad.2020911. View

Gupta S, Carmi S, Waldman Ben-Asher H, Tkacz I, Naboishchikov I, Michaeli S . Basal splicing factors regulate the stability of mature mRNAs in trypanosomes. J Biol Chem. 2013; 288(7):4991-5006. PMC: 3576102. DOI: 10.1074/jbc.M112.416578. View

Hartmann C, Benz C, Brems S, Ellis L, Luu V, Stewart M . Small trypanosome RNA-binding proteins TbUBP1 and TbUBP2 influence expression of F-box protein mRNAs in bloodstream trypanosomes. Eukaryot Cell. 2007; 6(11):1964-78. PMC: 2168414. DOI: 10.1128/EC.00279-07. View

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P . Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell. 2010; 141(1):129-41. PMC: 2861495. DOI: 10.1016/j.cell.2010.03.009. View

Estevez A, Lehner B, Sanderson C, Ruppert T, Clayton C . The roles of intersubunit interactions in exosome stability. J Biol Chem. 2003; 278(37):34943-51. DOI: 10.1074/jbc.M305333200. View

Song M, Li Y, Kiledjian M . Multiple mRNA decapping enzymes in mammalian cells. Mol Cell. 2010; 40(3):423-32. PMC: 2982215. DOI: 10.1016/j.molcel.2010.10.010. View

10.

Lu G, Hall T . Alternate modes of cognate RNA recognition by human PUMILIO proteins. Structure. 2011; 19(3):361-7. PMC: 3063405. DOI: 10.1016/j.str.2010.12.019. View

11.

Alibu V, Storm L, Haile S, Clayton C, Horn D . A doubly inducible system for RNA interference and rapid RNAi plasmid construction in Trypanosoma brucei. Mol Biochem Parasitol. 2004; 139(1):75-82. DOI: 10.1016/j.molbiopara.2004.10.002. View

12.

Kramer S, Queiroz R, Ellis L, Webb H, Hoheisel J, Clayton C . Heat shock causes a decrease in polysomes and the appearance of stress granules in trypanosomes independently of eIF2(alpha) phosphorylation at Thr169. J Cell Sci. 2008; 121(Pt 18):3002-14. PMC: 2871294. DOI: 10.1242/jcs.031823. View

13.

Olivas W, Parker R . The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast. EMBO J. 2000; 19(23):6602-11. PMC: 305854. DOI: 10.1093/emboj/19.23.6602. View

14.

Jensen B, Sivam D, Kifer C, Myler P, Parsons M . Widespread variation in transcript abundance within and across developmental stages of Trypanosoma brucei. BMC Genomics. 2009; 10:482. PMC: 2771046. DOI: 10.1186/1471-2164-10-482. View

15.

Gupta S, Kosti I, Plaut G, Pivko A, Tkacz I, Cohen-Chalamish S . The hnRNP F/H homologue of Trypanosoma brucei is differentially expressed in the two life cycle stages of the parasite and regulates splicing and mRNA stability. Nucleic Acids Res. 2013; 41(13):6577-94. PMC: 3711420. DOI: 10.1093/nar/gkt369. View

16.

Tong L, Lee S, Denu J . Hydrolase regulates NAD+ metabolites and modulates cellular redox. J Biol Chem. 2009; 284(17):11256-66. PMC: 2670130. DOI: 10.1074/jbc.M809790200. View

17.

Clayton C . The regulation of trypanosome gene expression by RNA-binding proteins. PLoS Pathog. 2013; 9(11):e1003680. PMC: 3820711. DOI: 10.1371/journal.ppat.1003680. View

18.

Haimovich G, Medina D, Causse S, Garber M, Millan-Zambrano G, Barkai O . Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis. Cell. 2013; 153(5):1000-11. DOI: 10.1016/j.cell.2013.05.012. View

19.

Keryer-Bibens C, Barreau C, Osborne H . Tethering of proteins to RNAs by bacteriophage proteins. Biol Cell. 2008; 100(2):125-38. DOI: 10.1042/BC20070067. View

20.

Kramer S, Carrington M . Trans-acting proteins regulating mRNA maturation, stability and translation in trypanosomatids. Trends Parasitol. 2010; 27(1):23-30. PMC: 3070815. DOI: 10.1016/j.pt.2010.06.011. View