An RNAi screen of the RRM-domain proteins of Trypanosoma brucei

Wurst, Martin; Robles, Ana I.; Po, June Y. T.; Luu, Van-Duc; Brems, Stefanie; Marentije, Mari; Stoitsova, Savrina; Quijada, Luis; Hoheisel, Jöerg; Stewart, Mhairi; Hartmann, Claudia; Clayton, Christine

doi:10.1016/j.molbiopara.2008.09.001

Cited by 28 publications

(22 citation statements)

References 14 publications

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“…Of special interest are the proteins RBP29, DRBD2, DRBD10, which are implicated in mRNA stability but no studies exist to date describing their function. These factors seem to be unrelated to known splicing factors, and most probably do not function in splicing (7,50,51). PUF proteins detected in this purification are also implicated in mRNA stability, translation regulation, and rRNA processing (52,53).…”

Section: Genes Affected By Splicing Factors and Their Splicing And Pomentioning

confidence: 88%

Basal Splicing Factors Regulate the Stability of Mature mRNAs in Trypanosomes

Gupta

Carmi

Ben‐Asher

et al. 2013

Journal of Biological Chemistry

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Background:Trypanosome trans-splicing depends on basal splicing factors such as U2AF35, U2FA65, and SF1. Results: Transcriptome analyses of RNAi-silenced cells of basal splicing factors reveal differential reliance on factors for trans-splicing and a role for the splicing factors in mRNA stability. Conclusion: Basal splicing factors regulate trans-splicing and mRNA stability. Significance: This is the first study to suggest that basal splicing factors regulate mRNA stability.

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Section: Genes Affected By Splicing Factors and Their Splicing And Pomentioning

confidence: 88%

Basal Splicing Factors Regulate the Stability of Mature mRNAs in Trypanosomes

Gupta

Carmi

Ben‐Asher

et al. 2013

Journal of Biological Chemistry

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“…31 paraflagellar rod proteins (some already in the first dataset) were added that had been identified in a comparative proteomics study of T. brucei cells lacking a paraflagellar rod [33]. To find proteins with a putative RNA-binding domain, we used the list from [59]. Proteins involved in mitotic spindle formation and cytokinesis were identified through a survey of the literature.…”

Section: Methodsmentioning

confidence: 99%

The Cell Cycle Regulated Transcriptome of Trypanosoma brucei

et al. 2011

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Progression of the eukaryotic cell cycle requires the regulation of hundreds of genes to ensure that they are expressed at the required times. Integral to cell cycle progression in yeast and animal cells are temporally controlled, progressive waves of transcription mediated by cell cycle-regulated transcription factors. However, in the kinetoplastids, a group of early-branching eukaryotes including many important pathogens, transcriptional regulation is almost completely absent, raising questions about the extent of cell-cycle regulation in these organisms and the mechanisms whereby regulation is achieved. Here, we analyse gene expression over the Trypanosoma brucei cell cycle, measuring changes in mRNA abundance on a transcriptome-wide scale. We developed a “double-cut” elutriation procedure to select unperturbed, highly synchronous cell populations from log-phase cultures, and compared this to synchronization by starvation. Transcriptome profiling over the cell cycle revealed the regulation of at least 430 genes. While only a minority were homologous to known cell cycle regulated transcripts in yeast or human, their functions correlated with the cellular processes occurring at the time of peak expression. We searched for potential target sites of RNA-binding proteins in these transcripts, which might earmark them for selective degradation or stabilization. Over-represented sequence motifs were found in several co-regulated transcript groups and were conserved in other kinetoplastids. Furthermore, we found evidence for cell-cycle regulation of a flagellar protein regulon with a highly conserved sequence motif, bearing similarity to consensus PUF-protein binding motifs. RNA sequence motifs that are functional in cell-cycle regulation were more widespread than previously expected and conserved within kinetoplastids. These findings highlight the central importance of post-transcriptional regulation in the proliferation of parasitic kinetoplastids.

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“…There are no functional data on DRBD2 and RBP23. 46 However, ALBA proteins associate with T. cruzi and T. brucei ribosomes. 47,48 Interestingly, MRP1 and MRP2 were also shown to be associated with TSR1.…”

Section: Tsr1 and Tsr1ip Affect The Stability Of Mrnamentioning

confidence: 99%

Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing inTrypanosoma brucei

Gupta¹,

Chikne²,

Eliaz³

et al. 2014

RNA Biology

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In trypanosomes, mRNas are processed by trans-splicing; in this process, a common exon, the spliced leader, is added to all mRNas from a small RNa donor, the spliced leader RNa (sL RNa). however, little is known regarding how this process is regulated. In this study, we investigated the function of two serine-arginine-rich proteins, TsR1 and TsR1IP, implicated in trans-splicing in Trypanosoma brucei. Depletion of these factors by RNai suggested their role in both cisand trans-splicing. Microarray was used to examine the transcriptome of the silenced cells. The level of hundreds of mRNas was changed, suggesting that these proteins have a role in regulating only a subset of T. brucei mRNas. Massspectrometry analyses of complexes associated with these proteins suggest that these factors function in mRNa stability, translation, and rRNa processing. We further demonstrate changes in the stability of mRNa as a result of depletion of the two TsR proteins. In addition, rRNa defects were observed under the depletion of U2aF35, TsR1, and TsR1IP, but not sF1, suggesting involvement of sR proteins in rRNa processing. ©2014 Landes Bioscience. Do not distribute 716RNa Biology Volume 11 Issue 6 among the hundreds of proteins present in the RNA polymerase II transcription complex, and are often loaded co-transcriptionally and accompany the fully spliced mRNA to the cytoplasm. 19 Since splice site consensus sequences are not sufficient to direct assembly of the spliceosome, sequences present in exons or introns such as exonic and intronic splicing enhancers (ESE and ISE), or exonic and intronic splicing silencers (ESS or ISS), are used to bind factors that regulate spliceosome assembly. SR proteins stabilize interactions between the U1 snRNP at the 5′ splice site and U2AF65 at the 3′ splice site. SR proteins are also known to bind to ESE and antagonize the activity of hnRNP proteins recognizing ESS. 20 In metazoa such as C. elegans, several SR proteins are essential, but others are not. 21 In mouse, many SR proteins are essential for life. 22 SR proteins have other functions in addition to their role in splicing, such as nuclear export, non-sense-mediated decay, and translation. SR proteins affect translation directly and indirectly. SF2/ASF was shown to associate with polyribosomes and to enhance translation, probably via release of 4E-BP, a competitive inhibitor of cap-dependent translation. 17 Recent studies support the role of SR proteins not only as splicing regulators, but also implicate these proteins in genome stability, chromatin binding, transcription elongation, mRNA stability, mRNA export, and translation (see review 23 ).The function of SR proteins is regulated by phosphorylation and de-phosphorylation. The RS domain is extensively phosphorylated on serine residues and this modification controls the localization of the protein. Mammalian SR proteins become dephosphorylated during the course of pre-mRNA processing, and promote mRNP transit through the nuclear pore complex. 24 SR proteins associate with the exon-junct...

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An RNAi screen of the RRM-domain proteins of Trypanosoma brucei

Cited by 28 publications

References 14 publications

Basal Splicing Factors Regulate the Stability of Mature mRNAs in Trypanosomes

Basal Splicing Factors Regulate the Stability of Mature mRNAs in Trypanosomes

The Cell Cycle Regulated Transcriptome of Trypanosoma brucei

Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing inTrypanosoma brucei

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