RBP38, a Novel RNA-Binding Protein from Trypanosomatid Mitochondria, Modulates RNA Stability

ABSTRACT We describe here the isolation and characterization of a novel RNA-binding protein, RBP38, from Leishmania tarentolae mitochondria. This protein does not contain any known RNA-binding motifs and is highly conserved among the trypanosomatids, but no homologues were found in other organisms. Recombinant LtRBP38 binds single and double-stranded (ds) RNA substrates with dissociation constants in the 100 nM range, as determined by fluorescence polarization analysis. Downregulation of expression of the homologous gene, TbRBP38, in procyclic Trypanosoma brucei by using conditional dsRNA interference resulted in 80% reduction of steady-state levels of RNAs transcribed from both maxicircle and minicircle DNA. In organello pulse-chase labeling experiments were used to determine the stability of RNAs in mitochondria that were depleted of TbRBP38. The half-life of metabolically labeled RNA decreased from ∼160 to ∼60 min after depletion. In contrast, there was no change in transcriptional activity. These observations suggest a role of RBP38 in stabilizing mitochondrial RNA.

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The Putative RNA-Binding Protein Nrp1 Promotes the Loading of Kinesin-14/Klp2 to the Mitotic Spindle and Is Sequestered Into Heat-Induced Protein Aggregates in Fission Yeast

10.20944/preprints202103.0452.v1 ◽

2021 ◽

Author(s):

Masashi Yukawa ◽

Mitsuki Ohishi ◽

Yusuke Yamada ◽

Takashi Toda

Keyword(s):

Fission Yeast ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Protein Aggregates ◽

Associated Proteins ◽

Spindle Microtubules ◽

The Stability ◽

And Function ◽

Post Transcriptional Regulation

Cells form a bipolar spindle during mitosis to ensure accurate chromosome segregation. Proper spindle architecture is established by a set of kinesin motors and microtubule-associated proteins. In most eukaryotes, kinesin-5 motors are essential for this process, and genetic or chemical inhibition of their activity leads to the emergence of monopolar spindles and cell death. However, these deficiencies can be rescued by simultaneous inactivation of kinesin-14 motors, as they counteract kinesin-5. We conducted detailed genetic analyses in fission yeast to understand the mechanisms driving spindle assembly in the absence of kinesin-5. Here we show that deletion of the nrp1 gene, which encodes a putative RNA-binding protein with unknown function, can rescue temperature sensitivity caused by cut7-22, a fission yeast kinesin-5 mutant. Interestingly, kinesin-14/Klp2 levels on the spindles in the cut7 mutants were significantly reduced by the nrp1 deletion, although the total levels of Klp2 and the stability of spindle microtubules remained unaffected. Moreover, RNA-binding motifs of Nrp1 are essential for its cytoplasmic localization and function. We have also found that a portion of Nrp1 is spatially and functionally sequestered by chaperone-based protein aggregates upon mild heat stress and limits cell division at high temperatures. We propose that Nrp1 might be involved in post-transcriptional regulation through its RNA-binding ability to promote the loading of Klp2 on the spindle microtubules.

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Isolation and Characterization of a Novel Drought Responsive Gene Encoding a Glycine-rich RNA-binding Protein in Malus prunifolia (Willd.) Borkh.

Plant Molecular Biology Reporter ◽

10.1007/s11105-010-0221-1 ◽

2010 ◽

Vol 29 (1) ◽

pp. 125-134 ◽

Cited By ~ 21

Author(s):

Shuncai Wang ◽

Dong Liang ◽

Shouguo Shi ◽

Fengwang Ma ◽

Huairui Shu ◽

...

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Gene Encoding ◽

Malus Prunifolia ◽

Isolation And Characterization ◽

Responsive Gene

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RNA Binding Protein Ybx2 Regulates RNA Stability During Cold-Induced Brown Fat Activation

Diabetes ◽

10.2337/db17-0655 ◽

2017 ◽

Vol 66 (12) ◽

pp. 2987-3000 ◽

Cited By ~ 7

Author(s):

Dan Xu ◽

Shaohai Xu ◽

Aung Maung Maung Kyaw ◽

Yen Ching Lim ◽

Sook Yoong Chia ◽

...

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Stability ◽

Rna Binding Protein ◽

Brown Fat

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Isolation and Characterization of Goldfish Y Box Protein, a Germ-cell-specific RNA-binding Protein

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1997.00854.x ◽

1997 ◽

Vol 249 (3) ◽

pp. 854-861 ◽

Cited By ~ 17

Author(s):

Yoshinao Katsu ◽

Masakane Yamashita ◽

Yoshitaka Nagahama

Keyword(s):

Germ Cell ◽

Rna Binding ◽

Binding Protein ◽

Protein A ◽

Rna Binding Protein ◽

Isolation And Characterization

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RNPC1, an RNA-binding protein and a target of the p53 family, is required for maintaining the stability of the basal and stress-induced p21 transcript

Genes & Development ◽

10.1101/gad.1463306 ◽

2006 ◽

Vol 20 (21) ◽

pp. 2961-2972 ◽

Cited By ~ 89

Author(s):

L. Shu ◽

W. Yan ◽

X. Chen

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

P53 Family ◽

The Stability

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Polyamines Regulate the Stability of Activating Transcription Factor-2 mRNA through RNA-binding Protein HuR in Intestinal Epithelial Cells

Molecular Biology of the Cell ◽

10.1091/mbc.e07-07-0675 ◽

2007 ◽

Vol 18 (11) ◽

pp. 4579-4590 ◽

Cited By ~ 55

Author(s):

Lan Xiao ◽

Jaladanki N. Rao ◽

Tongtong Zou ◽

Lan Liu ◽

Bernard S. Marasa ◽

...

Keyword(s):

Transcription Factor ◽

Rna Binding ◽

Binding Protein ◽

Critical Role ◽

Rna Binding Protein ◽

Gene Promoter ◽

Protein Levels ◽

Ribonucleoprotein Complexes ◽

Activating Transcription Factor ◽

The Stability

Maintenance of intestinal mucosal epithelial integrity requires polyamines that modulate the expression of various genes involved in cell proliferation and apoptosis. Recently, polyamines were shown to regulate the subcellular localization of the RNA-binding protein HuR, which stabilizes its target transcripts such as nucleophosmin and p53 mRNAs. The activating transcription factor-2 (ATF-2) mRNA encodes a member of the ATF/CRE-binding protein family of transcription factors and was computationally predicted to be a target of HuR. Here, we show that polyamines negatively regulate ATF-2 expression posttranscriptionally and that polyamine depletion stabilizes ATF-2 mRNA by enhancing the interaction of the 3′-untranslated region (UTR) of ATF-2 with cytoplasmic HuR. Decreasing cellular polyamines by inhibiting ornithine decarboxylase (ODC) with α-difluoromethylornithine increased the levels of ATF-2 mRNA and protein, whereas increasing polyamines by ectopic ODC overexpression repressed ATF-2 expression. Polyamine depletion did not alter transcription via the ATF-2 gene promoter but increased the stability of ATF-2 mRNA. Increased cytoplasmic HuR in polyamine-deficient cells formed ribonucleoprotein complexes with the endogenous ATF-2 mRNA and specifically bound to 3′-UTR of ATF-2 mRNA on multiple nonoverlapping 3′-UTR segments. Adenovirus-mediated HuR overexpression elevated ATF-2 mRNA and protein levels, whereas HuR silencing rendered the ATF-2 mRNA unstable and prevented increases in ATF-2 mRNA and protein. Furthermore, inhibition of ATF-2 expression prevented the increased resistance of polyamine-deficient cells to apoptosis induced by treatment with tumor necrosis factor-α and cycloheximide. These results indicate that polyamines modulate the stability of ATF-2 mRNA by altering cytoplasmic HuR levels and that polyamine-modulated ATF-2 expression plays a critical role in regulating epithelial apoptosis.

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Nuclear TARBP2 drives oncogenic dysregulation of RNA splicing and decay

10.1101/389213 ◽

2018 ◽

Author(s):

Lisa Fish ◽

Hoang C.B. Nguyen ◽

Steven Zhang ◽

Myles Hochman ◽

Brian D. Dill ◽

...

Keyword(s):

Gene Expression ◽

Lung Cancer ◽

Transcription Factor ◽

Rna Binding ◽

Binding Protein ◽

Intron Retention ◽

Rna Stability ◽

Rna Binding Protein ◽

List Type ◽

Gene Expression Control

SUMMARYPost-transcriptional regulation of RNA stability is a key step in gene expression control. We describe a regulatory program, mediated by the double-stranded RNA binding protein TARBP2, that controls RNA stability in the nucleus. TARBP2 binding to pre-mRNAs results in increased intron retention, subsequently leading to targeted degradation of TARBP2-bound transcripts. This is mediated by TARBP2 recruitment of the m6A RNA methylation machinery to its target transcripts, where deposition of m6A marks influences the recruitment of splicing regulators, inhibiting efficient splicing. Interactions between TARBP2 and the nucleoprotein TPR then promote degradation of these TARBP2-bound transcripts by the nuclear exosome. Additionally, analysis of clinical gene expression datasets revealed a functional role for this TARBP2 pathway in lung cancer. Using xenograft mouse models, we find that TARBP2 impacts tumor growth in the lung, and that this function is dependent on TARBP2-mediated destabilization of ABCA3 and FOXN3. Finally, we establish the transcription factor ZNF143 as an upstream regulator of TARBP2 expression.RESEARCH HIGHLIGHTSThe RNA-binding protein TARBP2 controls the stability of its target transcripts in the nucleusNuclear TARBP2 recruits the methyltransferase complex to deposit m6A marks on its target transcriptsTARBP2 and m6A-mediated interactions with splicing and nuclear RNA surveillance complexes result in target transcript intron retention and decay.Increased TARBP2 expression is associated with lung cancer and promotes lung cancer growthin vivo.The transcription factor ZNF143 drives oncogenic TARBP2 upregulation in lung cancer.

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