Full-length NF-κB repressing factor contains an XRN2 binding domain

NF-κB repressing factor (NKRF) was recently identified as an RNA binding protein that together with its associated proteins, the 5′–3′ exonuclease XRN2 and the helicase DHX15, is required to process the precursor ribosomal RNA. XRN2 is a multi-functional ribonuclease that is also involved in processing mRNAs, tRNAs and lncRNAs. The activity and stability of XRN2 are controlled by its binding partners, PAXT-1, CDKN2AIP and CDKN2AIPNL. In each case, these proteins interact with XRN2 via an XRN2 binding domain (XTBD), the structure and mode of action of which is highly conserved. Rather surprisingly, although NKRF interacts directly with XRN2, it was not predicted to contain such a domain, and NKRF's interaction with XRN2 was therefore unexplained. We have identified an alternative upstream AUG start codon within the transcript that encodes NKRF and demonstrate that the full-length form of NKRF contains an XTBD that is conserved across species. Our data suggest that NKRF is tethered in the nucleolus by binding directly to rRNA and that the XTBD in the N-terminal extension of NKRF is essential for the retention of XRN2 in this sub-organelle. Thus, we propose NKRF regulates the early steps of pre-rRNA processing during ribosome biogenesis by controlling the spatial distribution of XRN2 and our data provide further support for the XTBD as an XRN2 interacting motif.

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Faculty Opinions recommendation of Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.4747956.4641054 ◽

2010 ◽

Author(s):

Kathleen Hall

Keyword(s):

Ribosomal Rna ◽

Rna Binding ◽

Binding Domain ◽

Rna Recognition Motif ◽

Rna Recognition ◽

Recognition Motif ◽

Dead Box ◽

Rna Binding Domain

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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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Controlling the material properties and rRNA processing function of the nucleolus using light

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1903870116 ◽

2019 ◽

Vol 116 (35) ◽

pp. 17330-17335 ◽

Cited By ~ 17

Author(s):

Lian Zhu ◽

Tiffany M. Richardson ◽

Ludivine Wacheul ◽

Ming-Tzo Wei ◽

Marina Feric ◽

...

Keyword(s):

Phase Behavior ◽

Ribosomal Rna ◽

Material Properties ◽

Viscoelastic Properties ◽

Ribosome Biogenesis ◽

Threshold Concentration ◽

Rrna Processing ◽

Small Proteins ◽

Nucleolar Material ◽

Processing Steps

The nucleolus is a prominent nuclear condensate that plays a central role in ribosome biogenesis by facilitating the transcription and processing of nascent ribosomal RNA (rRNA). A number of studies have highlighted the active viscoelastic nature of the nucleolus, whose material properties and phase behavior are a consequence of underlying molecular interactions. However, the ways in which the material properties of the nucleolus impact its function in rRNA biogenesis are not understood. Here we utilize the Cry2olig optogenetic system to modulate the viscoelastic properties of the nucleolus. We show that above a threshold concentration of Cry2olig protein, the nucleolus can be gelled into a tightly linked, low mobility meshwork. Gelled nucleoli no longer coalesce and relax into spheres but nonetheless permit continued internal molecular mobility of small proteins. These changes in nucleolar material properties manifest in specific alterations in rRNA processing steps, including a buildup of larger rRNA precursors and a depletion of smaller rRNA precursors. We propose that the flux of processed rRNA may be actively tuned by the cell through modulating nucleolar material properties, which suggests the potential of materials-based approaches for therapeutic intervention in ribosomopathies.

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Intranucleolar sites of ribosome biogenesis defined by the localization of early binding ribosomal proteins

The Journal of Cell Biology ◽

10.1083/jcb.200612048 ◽

2007 ◽

Vol 177 (4) ◽

pp. 573-578 ◽

Cited By ~ 38

Author(s):

Tim Krüger ◽

Hanswalter Zentgraf ◽

Ulrich Scheer

Keyword(s):

Ribosomal Rna ◽

Ribosomal Proteins ◽

Live Cell Imaging ◽

Ribosome Biogenesis ◽

Cell Imaging ◽

Rrna Processing ◽

Dense Fibrillar Component ◽

Assembly Pathway ◽

Fibrillar Component ◽

Processing Steps

Considerable efforts are being undertaken to elucidate the processes of ribosome biogenesis. Although various preribosomal RNP complexes have been isolated and molecularly characterized, the order of ribosomal protein (r-protein) addition to the emerging ribosome subunits is largely unknown. Furthermore, the correlation between the ribosome assembly pathway and the structural organization of the dedicated ribosome factory, the nucleolus, is not well established. We have analyzed the nucleolar localization of several early binding r-proteins in human cells, applying various methods, including live-cell imaging and electron microscopy. We have located all examined r-proteins (S4, S6, S7, S9, S14, and L4) in the granular component (GC), which is the nucleolar region where later pre-ribosomal RNA (rRNA) processing steps take place. These results imply that early binding r-proteins do not assemble with nascent pre-rRNA transcripts in the dense fibrillar component (DFC), as is generally believed, and provide a link between r-protein assembly and the emergence of distinct granules at the DFC–GC interface.

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An RNA-binding switch drives ribosome biogenesis and tumorigenesis downstream of RAS oncogene

10.1101/2021.12.16.472890 ◽

2021 ◽

Author(s):

Muhammad S Azman ◽

Martin Dodel ◽

Federica Capraro ◽

Rupert Faraway ◽

Maria Dermit ◽

...

Keyword(s):

Gene Expression ◽

Ribosomal Rna ◽

Ribosome Biogenesis ◽

Rna Binding ◽

Binding Activity ◽

Ras Signaling ◽

Cancer Cell Proliferation ◽

Inhibit Tumor Growth ◽

Oncogenic Ras

Oncogenic RAS signaling reprograms gene expression through both transcriptional and post-transcriptional mechanisms. While transcriptional regulation downstream of RAS is relatively well-characterized, how RAS post-transcriptionally modulates gene expression to promote malignancy is unclear. Using quantitative RNA Interactome Capture analysis, we reveal that oncogenic RAS signaling reshapes the RNA-bound proteomic landscape of cancer cells, with a network of nuclear proteins centered around Nucleolin displaying enhanced RNA-binding activity. We show that Nucleolin is phosphorylated downstream of RAS, which increases its binding to pre-ribosomal-RNA (rRNA), boosts rRNA production, and promotes ribosome biogenesis. This Nucleolin-dependent enhancement of ribosome biogenesis is crucial for RAS-induced cancer cell proliferation, and can be targeted therapeutically to inhibit tumor growth. Our results reveal that oncogenic RAS signaling drives ribosome biogenesis by regulating the RNA-binding activity of Nucleolin, and highlights the crucial role of this process in RAS-mediated tumorigenesis.

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The chaperonin of the archaeon Sulfolobus solfataricus is an RNA-binding protein that participates in ribosomal RNA processing

The EMBO Journal ◽

10.1093/emboj/17.12.3471 ◽

1998 ◽

Vol 17 (12) ◽

pp. 3471-3477 ◽

Cited By ~ 33

Author(s):

D. Ruggero

Keyword(s):

Ribosomal Rna ◽

Rna Processing ◽

Rna Binding ◽

Binding Protein ◽

Sulfolobus Solfataricus ◽

Rna Binding Protein ◽

Ribosomal Rna Processing

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The RNA Binding Domain of Jerky Consists of Tandemly Arranged Helix-Turn-Helix/Homeodomain-Like Motifs and Binds Specific Sets of mRNAs

Molecular and Cellular Biology ◽

10.1128/mcb.23.12.4083-4093.2003 ◽

2003 ◽

Vol 23 (12) ◽

pp. 4083-4093 ◽

Cited By ~ 18

Author(s):

Wencheng Liu ◽

Jeremy Seto ◽

Etienne Sibille ◽

Miklos Toth

Keyword(s):

Dna Binding ◽

Ribosome Biogenesis ◽

Rna Binding ◽

Binding Domain ◽

Cellular Stress Response ◽

Rna Binding Domain ◽

Necessary And Sufficient ◽

Mrna Binding

ABSTRACT A deficit in the Jerky protein in mice causes recurrent seizures reminiscent of temporal lobe epilepsy. Jerky is present in mRNA particles in neurons. We show that the N-terminal 168 amino acids of Jerky are necessary and sufficient for mRNA binding. The binding domain is similar to the two tandemly arranged homeodomain-like helix-turn-helix DNA binding motifs of centromere binding protein B. The putative helix-turn-helix motifs of Jerky can also bind double-stranded DNA and represent a novel mammalian RNA/DNA binding domain. Microarray analysis identified mRNAs encoding proteins involved in ribosome assembly and cellular stress response that specifically bound to the RNA binding domain of Jerky both in vitro and in vivo. These data suggest that epileptogenesis in Jerky-deficient mice most likely involves pathways associated with ribosome biogenesis and neuronal survival and/or apoptosis.

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