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

2019 ◽  
Vol 116 (35) ◽  
pp. 17330-17335 ◽  
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.

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

2007 ◽  
Vol 177 (4) ◽  
pp. 573-578 ◽  
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.

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

2020 ◽  
Vol 477 (4) ◽  
pp. 773-786
Author(s):  
Jana Alexandrova ◽  
David Piñeiro ◽  
Rebekah Jukes-Jones ◽  
Ryan Mordue ◽  
Mark Stoneley ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Ribosome Biogenesis ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Binding Domain ◽  
Full Length ◽  
Start Codon ◽  
Rrna Processing ◽  
Binding Partners ◽  
Associated Proteins

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.

scholarly journals The nucleolar DExD/H protein Hel66 is involved in ribosome biogenesis in Trypanosoma brucei

2021 ◽  
Author(s):  
Majeed Bakari-Soale ◽  
Nonso Josephat Ikenge ◽  
Marion Scheibe ◽  
Falk Butter ◽  
Nicola Gail Jones ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Growth Defect ◽  
Rrna Processing ◽  
Ribosomal Subunits ◽  
Comprehensive Picture ◽  
Severe Growth Defect ◽  
H Protein ◽  
Severe Growth

The biosynthesis of ribosomes is a complex cellular process involving ribosomal RNA, ribosomal proteins and several further trans-acting factors. DExD/H box proteins constitute the largest family of trans-acting protein factors involved in this process. Several members of this protein family have been directly implicated in ribosome biogenesis in yeast. In trypanosomes, ribosome biogenesis differs in several features from the process described in yeast. Here, we have identified the DExD/H box helicase Hel66 as being involved in ribosome biogenesis. The protein is unique to Kinetoplastida, localises to the nucleolus and its depletion via RNAi caused a severe growth defect. Loss of the protein resulted in a decrease of global translation and accumulation of rRNA processing intermediates for both the small and large ribosomal subunits. Only a few factors involved in trypanosome rRNA biogenesis have been described so far and our findings contribute to gaining a more comprehensive picture of this essential process.

scholarly journals Viscoelastic RNA entanglement and advective flow underlie nucleolar form and function

2022 ◽  
Author(s):  
Joshua A Riback ◽  
Jorine M Eeftens ◽  
Daniel S.W. Lee ◽  
Sofia A Quinodoz ◽  
Lien Beckers ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Viscoelastic Properties ◽  
Ribosome Biogenesis ◽  
Quantitative Imaging ◽  
Advective Flow ◽  
Form And Function ◽  
Rrna Cleavage ◽  
And Function ◽  
Release Model ◽  
Nucleolar Function

The nucleolus facilitates transcription, processing, and assembly of ribosomal RNA (rRNA), the most abundant RNA in cells. Nucleolar function is facilitated by its multiphase liquid properties, but nucleolar fluidity and its connection to ribosome biogenesis remain unclear. Here, we used quantitative imaging, mathematical modeling, and pulse-chase nucleotide labelling to map nucleolar rRNA dynamics. Inconsistent with a purely diffusive process, rRNA steadily expands away from the transcriptional sites, moving in a slow (~1 Å/s), radially-directed fashion. This motion reflects the viscoelastic properties of a highly concentrated gel of entangled rRNA, whose constant polymerization drives steady outward flow. We propose a new viscoelastic rRNA release model, where nucleolar rRNA cleavage and processing reduce entanglement, fluidizing the nucleolar periphery to facilitate release of mature pre-ribosomal particles.

scholarly journals The Nucleolar DExD/H Protein Hel66 is Involved in Ribosome Biogenesis in Trypanosoma Brucei

2021 ◽  
Author(s):  
Majeed Bakari-Soale ◽  
Nonso Josephat Ikenga ◽  
Marion Scheibe ◽  
Falk Butter ◽  
Nicola Gail Jones ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Growth Defect ◽  
Rrna Processing ◽  
Ribosomal Subunits ◽  
Comprehensive Picture ◽  
Severe Growth Defect ◽  
H Protein ◽  
Severe Growth

Abstract The biosynthesis of ribosomes is a complex cellular process involving ribosomal RNA, ribosomal proteins and several further trans-acting factors. DExD/H box proteins constitute the largest family of trans-acting protein factors involved in this process. Several members of this protein family have been directly implicated in ribosome biogenesis in yeast. In trypanosomes, ribosome biogenesis differs in several features from the process described in yeast. Here, we have identified the DExD/H box helicase Hel66 as being involved in ribosome biogenesis. The protein is unique to Kinetoplastida, localises to the nucleolus and its depletion via RNAi caused a severe growth defect. Loss of the protein resulted in a decrease of global translation and accumulation of rRNA processing intermediates for both the small and large ribosomal subunits. Only a few factors involved in trypanosome rRNA biogenesis have been described so far and our findings contribute to gaining a more comprehensive picture of this essential process.

scholarly journals Fanconi anemia protein FANCI functions in ribosome biogenesis

2019 ◽  
Vol 116 (7) ◽  
pp. 2561-2570 ◽  
Author(s):  
Samuel B. Sondalle ◽  
Simonne Longerich ◽  
Lisa M. Ogawa ◽  
Patrick Sung ◽  
Susan J. Baserga
Keyword(s):  
Dna Repair ◽  
Fanconi Anemia ◽  
Ribosomal Rna ◽  
Ribosome Biogenesis ◽  
Bone Marrow Failure ◽  
Ribosomal Subunit ◽  
Rrna Processing ◽  
Large Ribosomal Subunit ◽  
Interstrand Cross Links ◽  
Cross Links

Fanconi anemia (FA) is a disease of DNA repair characterized by bone marrow failure and a reduced ability to remove DNA interstrand cross-links. Here, we provide evidence that the FA protein FANCI also functions in ribosome biogenesis, the process of making ribosomes that initiates in the nucleolus. We show that FANCI localizes to the nucleolus and is functionally and physically tied to the transcription of pre-ribosomal RNA (pre-rRNA) and to large ribosomal subunit (LSU) pre-rRNA processing independent of FANCD2. While FANCI is known to be monoubiquitinated when activated for DNA repair, we find that it is predominantly in the deubiquitinated state in the nucleolus, requiring the nucleoplasmic deubiquitinase (DUB) USP1 and the nucleolar DUB USP36. Our model suggests a possible dual pathophysiology for FA that includes defects in DNA repair and in ribosome biogenesis.

scholarly journals U3 small nuclear RNA can be psoralen-cross-linked in vivo to the 5' external transcribed spacer of pre-ribosomal-RNA

1989 ◽  
Vol 86 (17) ◽  
pp. 6523-6527 ◽  
Author(s):  
R L Maser ◽  
J P Calvet
Keyword(s):  
Ribosomal Rna ◽  
Ribosome Biogenesis ◽  
Rrna Processing ◽  
Small Nuclear Rna ◽  
Early Cleavage ◽  
External Transcribed Spacer ◽  
Nuclear Rna ◽  
Processing Event ◽  
Nucleolar Rna

U3 small nuclear RNA is hydrogen-bonded to high molecular weight nucleolar RNA and can be isolated from greater than 60S pre-ribosomal ribonucleoprotein particles, suggesting that it is involved in processing of ribosomal RNA precursors (pre-rRNA) or in ribosome biogenesis. Here we have used in vivo psoralen cross-linking to identify the region of pre-rRNA interacting with U3 RNA. Quantitative hybridization selection/depletion experiments with clones of rRNA-encoding DNA (rDNA) and cross-linked nuclear RNA showed that all of the cross-linked U3 RNA was associated with a region that includes the external transcribed spacer (ETS) at the 5' end of the human rRNA precursor. To further identify the site of interaction within the approximately 3.7-kilobase ETS, Southern blots of rDNA clones were sandwich-hybridized with cross-linked RNA and then probed for cross-linked U3 RNA. These experiments showed that U3 RNA was cross-linked to a 258-base sequence between nucleotides +438 and +695, just downstream of the ETS early cleavage site (+414). The localization of U3 to this region of the rRNA precursor was not expected from previous models for a base-paired U3-rRNA interaction and suggests that U3 plays a role in the initial pre-rRNA processing event.

scholarly journals The nucleolar DExD/H protein Hel66 is involved in ribosome biogenesis in Trypanosoma brucei

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Majeed Bakari-Soale ◽  
Nonso Josephat Ikenga ◽  
Marion Scheibe ◽  
Falk Butter ◽  
Nicola G. Jones ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Growth Defect ◽  
Rrna Processing ◽  
Ribosomal Subunits ◽  
Comprehensive Picture ◽  
Severe Growth Defect ◽  
H Protein ◽  
Severe Growth

AbstractThe biosynthesis of ribosomes is a complex cellular process involving ribosomal RNA, ribosomal proteins and several further trans-acting factors. DExD/H box proteins constitute the largest family of trans-acting protein factors involved in this process. Several members of this protein family have been directly implicated in ribosome biogenesis in yeast. In trypanosomes, ribosome biogenesis differs in several features from the process described in yeast. Here, we have identified the DExD/H box helicase Hel66 as being involved in ribosome biogenesis. The protein is unique to Kinetoplastida, localises to the nucleolus and its depletion via RNAi caused a severe growth defect. Loss of the protein resulted in a decrease of global translation and accumulation of rRNA processing intermediates for both the small and large ribosomal subunits. Only a few factors involved in trypanosome rRNA biogenesis have been described so far and our findings contribute to gaining a more comprehensive picture of this essential process.

Trans-acting factors in yeast pre-rRNA and pre-snoRNA processing

1995 ◽  
Vol 73 (11-12) ◽  
pp. 803-812 ◽  
Author(s):  
Denis Lafontaine ◽  
David Tollervey
Keyword(s):  
Rna Processing ◽  
Ribosome Biogenesis ◽  
Complex Mixture ◽  
Current View ◽  
Small Nucleolar Rnas ◽  
Rrna Processing ◽  
In Trans ◽  
Biochemical Analyses ◽  
Nucleolar Rnas ◽  
Processing Steps

The major intermediates in the pathway of pre-rRNA processing in yeast and other eukaryotes were originally identified by biochemical analyses. However, as a result of the analysis of the effects of mutations in trans-acting factors, the yeast pre-rRNA processing pathway is now characterized in far more detail than that of other eukaryotes. These analyses have led to the identification of processing sites and intermediates that were either too close in size or too short lived to be detected by biochemical analyses alone. In addition, it was generally unclear whether pre-rRNA processing steps were endonucleolytic or exonucleolytic; analyses of trans-acting factors is now revealing a complex mixture of endonucleolytic and exonucleolytic processing steps. Many of the small nucleolar RNAs (snoRNAs) are excised from larger precursors. Analyses of trans-acting factors are also revealing details of pre-snoRNA processing in yeast. Interestingly, factors involved in pre-snoRNA processing turn out to be components that also function in pre-rRNA processing, suggesting a potential mechanism for the coregulation of rRNA and snoRNA synthesis. In general, very little is known about the regulation of pre-rRNA processing steps. The best candidate for a system regulating specific pre-rRNA processing reactions has recently been revealed by the analysis of a yeast pre-RNA methylase. Here we will review recent data on the trans-acting factors involved in yeast ribosome synthesis and discuss how these analyses have contributed to our current view of this complex process.Key words: RNA processing, ribosome biogenesis, rRNA, exonuclease, methylation, yeast.

scholarly journals 3D Plotting of Silica/Collagen Xerogel Granules in an Alginate Matrix for Tissue-Engineered Bone Implants

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 830
Author(s):  
Sina Rößler ◽  
Andreas Brückner ◽  
Iris Kruppke ◽  
Hans-Peter Wiesmann ◽  
Thomas Hanke ◽  
...  
Keyword(s):  
Additive Manufacturing ◽  
Bone Regeneration ◽  
Material Properties ◽  
Viscoelastic Properties ◽  
Viscoelastic Behavior ◽  
Matrix Phase ◽  
Patient Specific ◽  
Active Player ◽  
Alginate Concentration ◽  
Alginate Matrix

Today, materials designed for bone regeneration are requested to be degradable and resorbable, bioactive, porous, and osteoconductive, as well as to be an active player in the bone-remodeling process. Multiphasic silica/collagen Xerogels were shown, earlier, to meet these requirements. The aim of the present study was to use these excellent material properties of silica/collagen Xerogels and to process them by additive manufacturing, in this case 3D plotting, to generate implants matching patient specific shapes of fractures or lesions. The concept is to have Xerogel granules as active major components embedded, to a large proportion, in a matrix that binds the granules in the scaffold. By using viscoelastic alginate as matrix, pastes of Xerogel granules were processed via 3D plotting. Moreover, alginate concentration was shown to be the key to a high content of irregularly shaped Xerogel granules embedded in a minimum of matrix phase. Both the alginate matrix and Xerogel granules were also shown to influence viscoelastic behavior of the paste, as well as the dimensionally stability of the scaffolds. In conclusion, 3D plotting of Xerogel granules was successfully established by using viscoelastic properties of alginate as matrix phase.

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