Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing in<i>Trypanosoma brucei</i>

Gupta, Sachin; Chikne, Vaibhav; Eliaz, Dror; Tkacz, Itai Dov; Naboishchikov, Ilana; Carmi, Shai; Ben‐Asher, Hiba Waldman; Michaeli, Shulamit

doi:10.4161/rna.29143

Cited by 39 publications

(41 citation statements)

References 92 publications

(121 reference statements)

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“…Data from Manger and Boothroyd ( 38 ) and our analysis (data not shown) indicated that TbRRM1 does not play a global role in trans -splicing. However, given its association with PTB2, we cannot exclude that TbRRM1 functions in splicing commitment for a subset of transcripts, analogous to some SR splicing factors in mammals and TSR1 in T. brucei ( 36 ).…”

Section: Discussionmentioning

confidence: 99%

“… T. brucei possesses at least two SR proteins, TbRRM1 (Tb927.2.4710) and TSR1 (Tb927.8.900), which were identified independently ( 34 , 35 ). TSR1 has recently been shown to modulate the splicing of a subset of transcripts and is considered an auxiliary factor in this process ( 36 ). In addition, three more SR proteins are predicted to be encoded in the genome (RBSR1 [Tb927.9.6870], RBSR2 [Tb927.7.1390], and RBSR3 [Tb927.3.5460]).…”

Section: Introductionmentioning

confidence: 99%

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Trypanosoma brucei RRM1 Is a Nuclear RNA-Binding Protein and Modulator of Chromatin Structure

Naguleswaran

Gunasekera

Schimanski

et al. 2015

mBio

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TbRRM1 of Trypanosoma brucei is a nucleoprotein that was previously identified in a search for splicing factors in T. brucei. We show that TbRRM1 associates with mRNAs and with the auxiliary splicing factor polypyrimidine tract-binding protein 2, but not with components of the core spliceosome. TbRRM1 also interacts with several retrotransposon hot spot (RHS) proteins and histones. RNA immunoprecipitation of a tagged form of TbRRM1 from procyclic (insect) form trypanosomes identified ca. 1,500 transcripts that were enriched and 3,000 transcripts that were underrepresented compared to cellular mRNA. Enriched transcripts encoded RNA-binding proteins, including TbRRM1 itself, several RHS transcripts, mRNAs with long coding regions, and a high proportion of stage-regulated mRNAs that are more highly expressed in bloodstream forms. Transcripts encoding ribosomal proteins, other factors involved in translation, and procyclic-specific transcripts were underrepresented. Knockdown of TbRRM1 by RNA interference caused widespread changes in mRNA abundance, but these changes did not correlate with the binding of the protein to transcripts, and most splice sites were unchanged, negating a general role for TbRRM1 in splice site selection. When changes in mRNA abundance were mapped across the genome, regions with many downregulated mRNAs were identified. Two regions were analyzed by chromatin immunoprecipitation, both of which exhibited increases in nucleosome occupancy upon TbRRM1 depletion. In addition, subjecting cells to heat shock resulted in translocation of TbRRM1 to the cytoplasm and compaction of chromatin, consistent with a second role for TbRRM1 in modulating chromatin structure.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Trypanosoma brucei RRM1 Is a Nuclear RNA-Binding Protein and Modulator of Chromatin Structure

Naguleswaran

Gunasekera

Schimanski

et al. 2015

mBio

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“…As a consequence of this arrangement, regulation of gene expression in trypanosomes is almost exclusively post-transcriptional: there are big differences between mRNAs in their processing efficiencies, decay rates, and translation (47)(48)(49). RNA-binding proteins have been shown to regulate specific trypanosome mRNA subsets, acting on splicing, mRNA decay, and / or translation (50)(51)(52). With one exception, however (53), the molecular mechanisms by which these proteins act are not yet known.…”

Section: Introductionmentioning

confidence: 99%

The suppressive cap-binding-complex factor 4EIP is required for normal differentiation

Clayton

Terrao

Marucha

et al. 2018

Preprint

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Summary/AbstractTrypanosoma brucei live in mammals as bloodstream forms and in the Tsetse midgut as procyclic forms. Differentiation from one form to the other proceeds via a growth-arrested stumpy form with low mRNA content and translation. The parasites have six eIF4Es and five eIF4Gs. EIF4E1 pairs with the mRNA-binding protein 4EIP but not with any EIF4G. EIF4E1 and 4EIP each inhibit expression when tethered to a reporter mRNA. The 4E-binding motif in 4EIP is required for the interaction with EIF4E1 both in vivo and in a 2-hybrid assay, but not for the suppressive activity of 4EIP when tethered. However, the suppressive activity of EIF4E1 when tethered requires 4EIP. Correspondingly, in growing bloodstream forms, 4EIP is preferentially associated with unstable mRNAs. Trypanosomes lacking 4EIP have a marginal growth disadvantage as cultured bloodstream or procyclic forms. Bloodstream forms without 4EIP cannot make differentiation-competent stumpy forms, but the defect can be complemented by a truncated 4EIP that does not interact with EIF4E1. Bloodstream forms lacking EIF4E1 have a growth defect but can differentiate. We suggest that 4EIP and EIF4E1 fine-tune mRNA levels in growing cells, and that 4EIP is required for mRNA suppression during differentiation to the stumpy form.

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“…Several SR proteins exist in T. brucei, among them: TSR1 (Ismaili et al 1999) and TSR1IP (Ismaili et al 2000), and one SR-related protein, TbRRM1 (RNA-binding protein RRM1) (Manger and Boothroyd 1998). TSR1 and TSR1IP have been shown to be involved in cis and trans-splicing, as well as in the regulation of mRNA stability of a subset of transcripts and in rRNA processing (Gupta et al 2014). Recently, it has been shown that TbRRM1 is involved in cell cycle regulation (Levy et al 2015), and both chromatin structure and transcriptome modulation (Naguleswaran et al 2015).…”

Section: Introductionmentioning

confidence: 99%

“…TSR1 and TSR1IP have been shown to be involved in cis and trans ‐splicing, as well as in the regulation of mRNA stability of a subset of transcripts and in rRNA processing (Gupta et al. ). Recently, it has been shown that TbRRM1 is involved in cell cycle regulation (Levy et al.…”

mentioning

confidence: 99%

The Trypanosoma brucei RNA‐Binding Protein TbRRM1 is Involved in the Transcription of a Subset of RNA Pol II‐Dependent Genes

Bañuelos

Levy

Níttolo

et al. 2019

J Eukaryotic Microbiology

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It has been long thought that RNA Polymerase (Pol) II transcriptional regulation does not operate in trypanosomes. However, recent reports have suggested that these organisms could regulate RNA Pol II transcription by epigenetic mechanisms. In this paper, we investigated the role of TbRRM1 in transcriptional regulation of RNA Pol II‐dependent genes by focusing both in genes located in a particular polycistronic transcription unit (PTU) and in the monocistronic units of the SL‐RNA genes. We showed that TbRRM1 is recruited throughout the PTU, with a higher presence on genes than intergenic regions. However, its depletion leads both to the decrease of nascent RNA and to chromatin compaction only of regions located distal to the main transcription start site. These findings suggest that TbRRM1 facilitates the RNA Pol II transcriptional elongation step by collaborating to maintain an open chromatin state in particular regions of the genome. Interestingly, the SL‐RNA genes do not recruit TbRRM1 and, after TbRRM1 knockdown, nascent SL‐RNAs accumulate while the chromatin state of these regions remains unchanged. Although it was previously suggested that TbRRM1 could regulate RNA Pol II‐driven genes, we provide here the first experimental evidence which involves TbRRM1 to transcriptional regulation.

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

Cited by 39 publications

References 92 publications

Trypanosoma brucei RRM1 Is a Nuclear RNA-Binding Protein and Modulator of Chromatin Structure

Trypanosoma brucei RRM1 Is a Nuclear RNA-Binding Protein and Modulator of Chromatin Structure

The suppressive cap-binding-complex factor 4EIP is required for normal differentiation

The Trypanosoma brucei RNA‐Binding Protein TbRRM1 is Involved in the Transcription of a Subset of RNA Pol II‐Dependent Genes

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