An <scp>Alba</scp>‐domain protein contributes to the stage‐regulated stability of amastin transcripts in <i><scp>L</scp>eishmania</i>

Dupé, Aurélien; Dumas, Carole; Papadopoulou, Barbara

doi:10.1111/mmi.12478

Cited by 43 publications

(50 citation statements)

References 66 publications

(95 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Also, DRBD13 has been demonstrated to negatively regulate mRNAs encoding for cell membrane-associated proteins via interaction with AREs of the target transcripts (Jha et al 2015). More recently, we showed that the Leishmania infantum Alba3 protein can stabilize the developmentally regulated amastin transcripts specifically in the amastigote stage upon binding to a U-rich element in the 3 ′ UTR (Dupé et al 2014).…”

Section: Introductionmentioning

confidence: 83%

“…Regulation of mRNA decay rates through interactions of RNA-binding proteins (RBPs) with cis-acting sequences in 3 ′ UTRs of trypanosomatid transcripts is central in determining the fate of mRNAs and thus fine-tuning developmental gene expression (McNicoll et al 2005;Bringaud et al 2007;Haile and Papadopoulou 2007;Haile et al 2008;Müller et al 2010b;Kramer 2012;Clayton 2013). Several RBPs, such as zinc finger proteins, Alba-domain proteins, and Pumilio (PUF) proteins, have been found to regulate mRNA stability in trypanosomatids (Clayton 2013;Dupé et al 2014).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The Pumilio-domain protein PUF6 contributes to SIDER2 retroposon-mediated mRNA decay in Leishmania

Azizi

Dumas

Papadopoulou

2017

RNA

Self Cite

View full text Add to dashboard Cite

Leishmania and other trypanosomatid protozoa lack control at the level of transcription initiation and regulate gene expression exclusively post-transcriptionally. We have reported previously that Leishmania harbors a unique class of short interspersed degenerate retroposons (SIDERs) that are predominantly located within 3 ′ ′ ′ ′ ′ UTRs and play a major role in post-transcriptional control. We have shown that members of the SIDER2 subfamily initiate mRNA decay through endonucleolytic cleavage within the second conserved 79-nt signature sequence of SIDER2 retroposons. Here, we have developed an optimized MS2 coat protein tethering system to capture trans-acting factor(s) regulating SIDER2-mediated mRNA decay. Tethering of the MS2 coat protein to a reporter RNA harboring two MS2 stem-loop aptamers and the cognate SIDER2-containing 3 ′ ′ ′ ′ ′ UTR in combination with immunoprecipitation and mass spectrometry analysis led to the identification of RNA-binding proteins with known functions in mRNA decay. Among the candidate SIDER2-interacting proteins that were individually tethered to a SIDER2 reporter RNA, the Pumilio-domain protein PUF6 was shown to enhance degradation and reduce transcript half-life. Furthermore, we showed that PUF6 binds to SIDER2 sequences that include the regulatory 79-nt signature motif, hence contributing to the mRNA decay process. Consistent with a role of PUF6 in SIDER2-mediated decay, genetic inactivation of PUF6 resulted in increased accumulation and higher stability of endogenous SIDER2-bearing transcripts. Overall, these studies provide new insights into regulated mRNA decay pathways in Leishmania controlled by SIDER2 retroposons and propose a broader role for PUF proteins in mRNA decay within the eukaryotic kingdom.

show abstract

Section: Introductionmentioning

confidence: 83%

Section: Introductionmentioning

confidence: 99%

The Pumilio-domain protein PUF6 contributes to SIDER2 retroposon-mediated mRNA decay in Leishmania

Azizi

Dumas

Papadopoulou

2017

RNA

Self Cite

View full text Add to dashboard Cite

show abstract

“…To isolate AMA(LD) parasites in vivo, 1x10 7 serum-treated META L.mexicana cells were injected in rumps of [8][9][10][11][12] week old Balb/c mice (Charles River, UK). After 4 months the mice were sacrificed and the lesions harvested as described [6,24].…”

Section: Mice Infectionsmentioning

confidence: 99%

“…For parasite lifecycle progression, both metacyclogenesis (procyclic to metacyclic promastigote) and amastigogenesis (metacyclic promastigote to amastigote) differentiation processes require tightly coordinated gene regulation [2]. To date, many ciselements but strikingly few trans-regulators have been implicated in Leishmania developmental progression [3][4][5][6][7][8][9][10][11]. The identification of Leishmania trans-regulators that bind mRNAs in a stage-specific manner lends vital insight into the cellular processes which promote and enable parasite survival.…”

Section: Introductionmentioning

confidence: 99%

The mRNA-bound proteome ofLeishmania mexicana: novel genetic insight into an ancient parasite

Pablos

Ferreira

Dowle

et al. 2019

Preprint

View full text Add to dashboard Cite

Leishmania parasite infections, termed the leishmaniases, cause significant global infectious disease burden. The lifecycle of the parasite embodies three main stages that require precise coordination of gene regulation to survive environmental shifts between sandfly and mammalian hosts. Constitutive transcription in kinetoplastid parasites means that gene regulation is overwhelmingly reliant on post-transcriptional mechanisms, yet strikingly few Leishmania trans-regulators are known. Utilizing optimised crosslinking and deep, quantified mass spectrometry, we present a comprehensive analysis of 1,400 mRNA binding proteins (mRBPs) and whole cell proteomes from the three main Leishmania lifecycle stages.Supporting the validity, while the crosslinked RBPome is magnitudes more enriched the protein identities of the crosslinked and non-crosslinked RBPomes were nearly identical.Moreover, multiple candidate RBPs were endogenously tagged and found to associate with discrete mRNA target pools in a stage-specific manner. Results indicate that in L.mexicana parasites, mRNA levels are not a strong predictor of the whole cell expression or RNA binding potential of encoded proteins. Evidence includes a low correlation between transcript and corresponding protein expression and stage-specific variation in protein expression versus RNA binding potential. Unsurprisingly, RNA binding protein enrichment correlates strongly with relative replication efficiency of the specific lifecycle stage. Our study is the first to quantitatively define and compare the mRBPome of multiple stages in kinetoplastid parasites. It provides novel, in-depth insight into the trans-regulatory mRNA:Protein (mRNP) complexes that drive Leishmania parasite lifecycle progression.

show abstract

“…Cis -acting motifs within 3'UTRs of Leishmania transcripts have been shown to play major roles in regulating mRNA stability and translation [8–15]. We have previously identified and characterized a large class of cis -acting elements in Leishmania , SIDERs for S hort I nterspersed DE generate R etroposons [11].…”

Section: Introductionmentioning

confidence: 99%

RNA secondary structure and nucleotide composition of the conserved hallmark sequence of Leishmania SIDER2 retroposons are essential for endonucleolytic cleavage and mRNA degradation

et al. 2017

Self Cite

View full text Add to dashboard Cite

We have reported previously that Short Interspersed Degenerate Retroposons of the SIDER2 subfamily, largely located within 3'UTRs of Leishmania transcripts, promote rapid turnover of mRNAs through endonucleolytic cleavage within the highly conserved second tandem 79-nt hallmark sequence (79-nt SII). Here, we used site-directed mutagenesis and in silico RNA structural studies to delineate the cis-acting requirements within 79-nt SII for cleavage and mRNA degradation. The putative cleavage site(s) and other nucleotides predicted to alter the RNA secondary structure of 79-nt SII were either deleted or mutated and their effect on mRNA turnover was monitored using a gene reporter system. We found that short deletions of 8-nt spanning the two predicted cleavage sites block degradation of SIDER2-containing transcripts, leading to mRNA accumulation. Furthermore, single or double substitutions of the dinucleotides targeted for cleavage as well as mutations altering the predicted RNA secondary structure encompassing both cleavage sites also prevent mRNA degradation, confirming that these dinucleotides are the bona fide cleavage sites. In line with these results, we show that stage-regulated SIDER2 inactivation correlates with the absence of endonucleolytic cleavage. Overall, these data demonstrate that both cleavage sites within the conserved 79-nt SII as well as RNA folding in this region are essential for SIDER2-mediated mRNA decay, and further support that SIDER2-harboring transcripts are targeted for degradation by endonucleolytic cleavage.

show abstract

An Alba‐domain protein contributes to the stage‐regulated stability of amastin transcripts in Leishmania

Cited by 43 publications

References 66 publications

The Pumilio-domain protein PUF6 contributes to SIDER2 retroposon-mediated mRNA decay in Leishmania

The Pumilio-domain protein PUF6 contributes to SIDER2 retroposon-mediated mRNA decay in Leishmania

The mRNA-bound proteome ofLeishmania mexicana: novel genetic insight into an ancient parasite

RNA secondary structure and nucleotide composition of the conserved hallmark sequence of Leishmania SIDER2 retroposons are essential for endonucleolytic cleavage and mRNA degradation

Contact Info

Product

Resources

About