1
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González-Arzola K. The nucleolus: Coordinating stress response and genomic stability. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195029. [PMID: 38642633 DOI: 10.1016/j.bbagrm.2024.195029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
The perception that the nucleoli are merely the organelles where ribosome biogenesis occurs is challenged. Only around 30 % of nucleolar proteins are solely involved in producing ribosomes. Instead, the nucleolus plays a critical role in controlling protein trafficking during stress and, according to its dynamic nature, undergoes continuous protein exchange with nucleoplasm under various cellular stressors. Hence, the concept of nucleolar stress has evolved as cellular insults that disrupt the structure and function of the nucleolus. Considering the emerging role of this organelle in DNA repair and the fact that rDNAs are the most fragile genomic loci, therapies targeting the nucleoli are increasingly being developed. Besides, drugs that target ribosome synthesis and induce nucleolar stress can be used in cancer therapy. In contrast, agents that regulate nucleolar activity may be a potential treatment for neurodegeneration caused by abnormal protein accumulation in the nucleolus. Here, I explore the roles of nucleoli beyond their ribosomal functions, highlighting the factors triggering nucleolar stress and their impact on genomic stability.
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Affiliation(s)
- Katiuska González-Arzola
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain.
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2
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Valyaeva AA, Sheval EV. Nonspecific Interactions in Transcription Regulation and Organization of Transcriptional Condensates. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:688-700. [PMID: 38831505 DOI: 10.1134/s0006297924040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 06/05/2024]
Abstract
Eukaryotic cells are characterized by a high degree of compartmentalization of their internal contents, which ensures precise and controlled regulation of intracellular processes. During many processes, including different stages of transcription, dynamic membraneless compartments termed biomolecular condensates are formed. Transcription condensates contain various transcription factors and RNA polymerase and are formed by high- and low-specificity interactions between the proteins, DNA, and nearby RNA. This review discusses recent data demonstrating important role of nonspecific multivalent protein-protein and RNA-protein interactions in organization and regulation of transcription.
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Affiliation(s)
- Anna A Valyaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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3
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Lafontaine DLJ. When two became three: Shaping the nucleolus with Treacle. Cell Rep 2023; 42:113060. [PMID: 37651232 DOI: 10.1016/j.celrep.2023.113060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023] Open
Abstract
The nucleolus is a multiphase biomolecular condensate responsible for the initial steps of ribosome biogenesis. Jaberi-Lashkari et al.1 report that Treacle, a protein associated with a craniofacial distortion disease, played an evolutionary role in the spatial specialization of the nucleolus.
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4
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Jaberi-Lashkari N, Lee B, Aryan F, Calo E. An evolutionarily nascent architecture underlying the formation and emergence of biomolecular condensates. Cell Rep 2023; 42:112955. [PMID: 37586369 PMCID: PMC10529244 DOI: 10.1016/j.celrep.2023.112955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/15/2023] [Accepted: 07/24/2023] [Indexed: 08/18/2023] Open
Abstract
Biomolecular condensates are implicated in core cellular processes such as gene regulation and ribosome biogenesis. Although the architecture of biomolecular condensates is thought to rely on collective interactions between many components, it is unclear how the collective interactions required for their formation emerge during evolution. Here, we show that the structure and evolution of a recently emerged biomolecular condensate, the nucleolar fibrillar center (FC), is explained by a single self-assembling scaffold, TCOF1. TCOF1 is necessary to form the FC, and it structurally defines the FC through self-assembly mediated by homotypic interactions of serine/glutamate-rich low-complexity regions (LCRs). Finally, introduction of TCOF1 into a species lacking the FC is sufficient to form an FC-like biomolecular condensate. By demonstrating that a recently emerged biomolecular condensate is built on a simple architecture determined by a single self-assembling protein, our work provides a compelling mechanism by which biomolecular condensates can emerge in the tree of life.
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Affiliation(s)
- Nima Jaberi-Lashkari
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Byron Lee
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Fardin Aryan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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5
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Lin S, Rajan S, Lemberg S, Altawil M, Anderson K, Bryant R, Cappeta S, Chin B, Hamdan I, Hamer A, Hyzny R, Karp A, Lee D, Lim A, Nayak M, Palaniappan V, Park S, Satishkumar S, Seth A, Sri Dasari U, Toppari E, Vyas A, Walker J, Weston E, Zafar A, Zielke C, Mahabeleshwar GH, Tartakoff AM. Production of nascent ribosome precursors within the nucleolar microenvironment of Saccharomyces cerevisiae. Genetics 2022; 221:iyac070. [PMID: 35657327 PMCID: PMC9252279 DOI: 10.1093/genetics/iyac070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
35S rRNA transcripts include a 5'-external transcribed spacer followed by rRNAs of the small and large ribosomal subunits. Their processing yields massive precursors that include dozens of assembly factor proteins. In Saccharomyces cerevisiae, nucleolar assembly factors form 2 coaxial layers/volumes around ribosomal DNA. Most of these factors are cyclically recruited from a latent state to an operative state, and are extensively conserved. The layers match, at least approximately, known subcompartments found in higher eukaryotic cells. ∼80% of assembly factors are essential. The number of copies of these assembly factors is comparable to the number of nascent transcripts. Moreover, they exhibit "isoelectric balance," with RNA-binding candidate "nucleator" assembly factors being notably basic. The physical properties of pre-small subunit and pre-large subunit assembly factors are similar, as are their 19 motif signatures detected by hierarchical clustering, unlike motif signatures of the 5'-external transcribed spacer rRNP. Additionally, many assembly factors lack shared motifs. Taken together with the progression of rRNP composition during subunit maturation, and the realization that the ribosomal DNA cable is initially bathed in a subunit-nonspecific assembly factor reservoir/microenvironment, we propose a "3-step subdomain assembly model": Step (1): predominantly basic assembly factors sequentially nucleate sites along nascent rRNA; Step (2): the resulting rRNPs recruit numerous less basic assembly factors along with notably basic ribosomal proteins; Step (3): rRNPs in nearby subdomains consolidate. Cleavages of rRNA then promote release of rRNPs to the nucleoplasm, likely facilitated by the persistence of assembly factors that were already associated with nucleolar precursors.
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Affiliation(s)
- Samantha Lin
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Suchita Rajan
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sofia Lemberg
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mark Altawil
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Katherine Anderson
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ruth Bryant
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sebastian Cappeta
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Brandon Chin
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Isabella Hamdan
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Annelise Hamer
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Rachel Hyzny
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Andrew Karp
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Daniel Lee
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alexandria Lim
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Medha Nayak
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Vishnu Palaniappan
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Soomin Park
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sarika Satishkumar
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Anika Seth
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Uva Sri Dasari
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Emili Toppari
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ayush Vyas
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Julianne Walker
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Evan Weston
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Atif Zafar
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Cecelia Zielke
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ganapati H Mahabeleshwar
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alan M Tartakoff
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
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6
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Ryu JK, Hwang DE, Choi JM. Current Understanding of Molecular Phase Separation in Chromosomes. Int J Mol Sci 2021; 22:10736. [PMID: 34639077 PMCID: PMC8509192 DOI: 10.3390/ijms221910736] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular phase separation denotes the demixing of a specific set of intracellular components without membrane encapsulation. Recent studies have found that biomolecular phase separation is involved in a wide range of cellular processes. In particular, phase separation is involved in the formation and regulation of chromosome structures at various levels. Here, we review the current understanding of biomolecular phase separation related to chromosomes. First, we discuss the fundamental principles of phase separation and introduce several examples of nuclear/chromosomal biomolecular assemblies formed by phase separation. We also briefly explain the experimental and computational methods used to study phase separation in chromosomes. Finally, we discuss a recent phase separation model, termed bridging-induced phase separation (BIPS), which can explain the formation of local chromosome structures.
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Affiliation(s)
- Je-Kyung Ryu
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Da-Eun Hwang
- Department of Chemistry, Pusan National University, Busan 46241, Korea;
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea;
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7
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Visualization of Chromatin in the Yeast Nucleus and Nucleolus Using Hyperosmotic Shock. Int J Mol Sci 2021; 22:ijms22031132. [PMID: 33498839 PMCID: PMC7866036 DOI: 10.3390/ijms22031132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/15/2021] [Accepted: 01/17/2021] [Indexed: 12/12/2022] Open
Abstract
Unlike in most eukaryotic cells, the genetic information of budding yeast in the exponential growth phase is only present in the form of decondensed chromatin, a configuration that does not allow its visualization in cell nuclei conventionally prepared for transmission electron microscopy. In this work, we studied the distribution of chromatin and its relationships to the nucleolus using different cytochemical and immunocytological approaches applied to yeast cells subjected to hyperosmotic shock. Our results show that osmotic shock induces the formation of heterochromatin patches in the nucleoplasm and intranucleolar regions of the yeast nucleus. In the nucleolus, we further revealed the presence of osmotic shock-resistant DNA in the fibrillar cords which, in places, take on a pinnate appearance reminiscent of ribosomal genes in active transcription as observed after molecular spreading ("Christmas trees"). We also identified chromatin-associated granules whose size, composition and behaviour after osmotic shock are reminiscent of that of mammalian perichromatin granules. Altogether, these data reveal that it is possible to visualize heterochromatin in yeast and suggest that the yeast nucleus displays a less-effective compartmentalized organization than that of mammals.
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8
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Davidian A, Koshel E, Dyomin A, Galkina S, Saifitdinova A, Gaginskaya E. On some structural and evolutionary aspects of rDNA amplification in oogenesis of Trachemys scripta turtles. Cell Tissue Res 2020; 383:853-864. [PMID: 32897424 DOI: 10.1007/s00441-020-03282-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
The features of rDNA amplification have been studied in oocytes of the red-eared slider Trachemys scripta using a number of specific histochemical and cytomolecular methods. A single nucleolus in early diplotene oocytes is associated with the nucleolus organizer region (NOR). With oocyte growth, the number of nucleoli increases dramatically and reaches hundreds by the lampbrush chromosome stage (pre-vitellogenesis). RNA-polymerase I, fibrillarin, and PCNA immunodetection in the amplified nucleoli and FISH of the 5'ETS probe to the oocyte nuclear content suggest pre-rRNA and rDNA synthesis in the nucleoli at all stages studied. This implies a continuous reproduction of the nucleoli during oocyte development from early diplotene up to vitellogenesis. The data obtained offer a different way for rDNA amplification and formation of extrachromosomal nucleoli in turtle oocytes compared with the amplified nucleoli formation in amphibian and fish oocytes. In the Sauropsida clade of Archelosauria, which includes turtles, crocodiles, and birds, rDNA function is known to be suppressed in avian oogenesis during the lampbrush stage (Gaginskaya et al. in Cytogenet Genome Res 124:251-267, 2009).
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Affiliation(s)
- Asya Davidian
- St Petersburg University, St Petersburg, 199034, Russia
| | | | - Alexander Dyomin
- St Petersburg University, St Petersburg, 199034, Russia.,Saratov State Medical University, Saratov, 410000, Russia
| | | | - Alsu Saifitdinova
- Herzen State Pedagogical University of Russia, St Petersburg, 191186, Russia
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9
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Abstract
The nucleolus is the most prominent nuclear body and serves a fundamentally important biological role as a site of ribonucleoprotein particle assembly, primarily dedicated to ribosome biogenesis. Despite being one of the first intracellular structures visualized historically, the biophysical rules governing its assembly and function are only starting to become clear. Recent studies have provided increasing support for the concept that the nucleolus represents a multilayered biomolecular condensate, whose formation by liquid-liquid phase separation (LLPS) facilitates the initial steps of ribosome biogenesis and other functions. Here, we review these biophysical insights in the context of the molecular and cell biology of the nucleolus. We discuss how nucleolar function is linked to its organization as a multiphase condensate and how dysregulation of this organization could provide insights into still poorly understood aspects of nucleolus-associated diseases, including cancer, ribosomopathies and neurodegeneration as well as ageing. We suggest that the LLPS model provides the starting point for a unifying quantitative framework for the assembly, structural maintenance and function of the nucleolus, with implications for gene regulation and ribonucleoprotein particle assembly throughout the nucleus. The LLPS concept is also likely useful in designing new therapeutic strategies to target nucleolar dysfunction.
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10
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Bartholomé O, Franck C, Piscicelli P, Lalun N, Defourny J, Renauld J, Thelen N, Lamaye F, Ploton D, Thiry M. Relationships between the structural and functional organization of the turtle cell nucleolus. J Struct Biol 2019; 208:107398. [PMID: 31585176 DOI: 10.1016/j.jsb.2019.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/21/2019] [Accepted: 09/27/2019] [Indexed: 12/30/2022]
Abstract
The nucleolus is a multifunctional structure of the eukaryotic cell nucleus. However, its primary role is ribosome formation. Although the factors and mechanisms involved in ribogenesis are well conserved in eukaryotes, two types of nucleoli have been observed under the electron microscope: a tricompartmentalized nucleolus in amniotes and a bicompartmentalized nucleolus in other species. A recent study has also revealed that turtles, although belonging to amniotes, displayed a nucleolus with bipartite organization, suggesting that this reptile group may have carried out a reversion phenomenon during evolution. In this study, we examine in great detail the functional organization of the turtle nucleolus. In liver and spleen cells cultured in vitro, we confirm that the turtle nucleolus is mainly formed by two components: a fibrillar zone surrounded by a granular zone. We further show that the fibrillar zone includes densely-contrasted strands, which are positive after silver-stained Nucleolar Organizer Region (Ag-NOR) staining and DNA labelling. We also reveal that the dense strands condensed into a very compact mass within the fibrillar zone after a treatment with actinomycin D or 5,6-dichlorobenzimidazole riboside. Finally, by using pulse-chase experiments with BrUTP, three-dimensional image reconstructions of confocal optical sections, and electron microscopy analysis of ultrathin sections, we show that the topological and spatial dynamics of rRNA within the nucleolus extend from upstream binding factor (UBF)-positive sites in the fibrillar zone to the granular zone, without ever releasing the positive sites for the UBF. Together, these results seem to clearly indicate that the compartmentalization of the turtle nucleolus into two main components reflects a less orderly organization of ribosome formation.
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Affiliation(s)
- Odile Bartholomé
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Claire Franck
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Patricia Piscicelli
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Nathalie Lalun
- UMRCNRS 6237, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Jean Defourny
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Justine Renauld
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Nicolas Thelen
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Françoise Lamaye
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Dominique Ploton
- UMRCNRS 6237, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Marc Thiry
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium.
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11
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Tchelidze P, Kaplan H, Terryn C, Lalun N, Ploton D, Thiry M. Electron tomography reveals changes in spatial distribution of UBTF1 and UBTF2 isoforms within nucleolar components during rRNA synthesis inhibition. J Struct Biol 2019; 208:191-204. [PMID: 31479756 DOI: 10.1016/j.jsb.2019.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/01/2022]
Abstract
Upstream binding transcription factor (UBTF) is a co-regulator of RNA polymerase I by constituting an initiation complex on rRNA genes. UBTF plays a role in rDNA bending and its maintenance in "open" state. It exists as two splicing variants, UBTF1 and UBTF2, which cannot be discerned with antibodies raised against UBTF. We investigated the ultrastructural localization of each variant in cells synthesizing GFP-tagged UBTF1 or UBTF2 by using anti-GFP antibodies and pre-embedding nanogold strategy. Detailed 3D distribution of UBTF1 and 2 was also studied by electron tomography. In control cells, the two isoforms are very abundant within fibrillar centers, but their repartition strongly differs. Electron tomography shows that UBTF1 is disposed as fibrils that are folded in coils whereas UBTF2 is localized homogenously, preferentially at their cortical area. As UBTF is a useful marker to trace rDNA genes, we used these data to improve our previous model of 3D organization of active transcribing rDNA gene within fibrillar centers. Finally, when rRNA synthesis is inhibited during actinomycin D treatment or entry in mitosis, UBTF1 and UBTF2 show a similar distribution along extended 3D loop-like structures. Altogether these data suggest new roles for UBTF1 and UBTF2 isoforms in the organization of active and inactive rDNA genes.
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Affiliation(s)
- Pavel Tchelidze
- Faculty of Health, Eastern European University, Tbilisi, Georgia
| | - Hervé Kaplan
- Université de Reims Champagne Ardenne, Reims, France
| | - Christine Terryn
- Platform of Cellular and Tissular Imaging (PICT), Université de Reims Champagne Ardenne, Reims, France
| | - Nathalie Lalun
- UMR-S 1250 INSERM, Université de Reims Champagne Ardenne, France
| | - Dominique Ploton
- BioSpecT, EA 7506, Université de Reims Champagne Ardenne, France
| | - Marc Thiry
- Unit of Cell and Tissue Biology, GIGA-Neurosciences, University of Liège, Liège, Belgium.
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12
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Mier P, Pérez-Pulido AJ, Reynaud EG, Andrade-Navarro MA. Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family. PLoS One 2017; 12:e0169750. [PMID: 28072865 PMCID: PMC5224878 DOI: 10.1371/journal.pone.0169750] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/21/2016] [Indexed: 01/07/2023] Open
Abstract
Reconstructing the transition from a single compartment bacterium to a highly compartmentalized eukaryotic cell is one of the most studied problems of evolutionary cell biology. However, timing and details of the establishment of compartmentalization are unclear and difficult to assess. Here, we propose the use of molecular markers specific to cellular compartments to set up a framework to advance the understanding of this complex intracellular process. Specifically, we use a protein family related to ribosome biogenesis, YRG (YlqF related GTPases), whose evolution is linked to the establishment of cellular compartments, leveraging the current genomic data. We analyzed orthologous proteins of the YRG family in a set of 171 proteomes for a total of 370 proteins. We identified ten YRG protein subfamilies that can be associated to six subcellular compartments (nuclear bodies, nucleolus, nucleus, cytosol, mitochondria, and chloroplast), and which were found in archaeal, bacterial and eukaryotic proteomes. Our analysis reveals organism streamlining related events in specific taxonomic groups such as Fungi. We conclude that the YRG family could be used as a compartmentalization marker, which could help to trace the evolutionary path relating cellular compartments with ribosome biogenesis.
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Affiliation(s)
- Pablo Mier
- Institute of Molecular Biology (IMB), Faculty of Biology, Johannes-Gutenberg University of Mainz, Mainz, Germany
- * E-mail:
| | - Antonio J. Pérez-Pulido
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, Sevilla, Spain
| | - Emmanuel G. Reynaud
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Miguel A. Andrade-Navarro
- Institute of Molecular Biology (IMB), Faculty of Biology, Johannes-Gutenberg University of Mainz, Mainz, Germany
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13
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Abstract
Here, we describe a method for locating DNA on ultrathin sections. This technique is compatible with all usual fixation and embedding procedures and can be combined with cytochemical methods. Ultrathin sections are incubated in a medium containing terminal deoxynucleotidyl transferase (TdT) and various non-isotopic nucleotide analogs. The labeled nucleotides bound to the surface of ultrathin sections are then visualized by an indirect immunogold labeling technique. This high-resolution method provides a powerful tool for pinpointing the precise location of DNA within biological material, even where DNA is present in very low amounts.
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Affiliation(s)
- Nicolas Thelen
- Giga Neurosciences, Department of Life Sciences, Laboratory of Cell Biology, University of Liège, Quartier Hôpital, 15 Avenue Hippocrate (B36), 4000, Liege, Belgium
| | - Marc Thiry
- Giga Neurosciences, Department of Life Sciences, Laboratory of Cell Biology, University of Liège, Quartier Hôpital, 15 Avenue Hippocrate (B36), 4000, Liege, Belgium.
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14
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Scott DD, Oeffinger M. Nucleolin and nucleophosmin: nucleolar proteins with multiple functions in DNA repair. Biochem Cell Biol 2016; 94:419-432. [PMID: 27673355 DOI: 10.1139/bcb-2016-0068] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The nucleolus represents a highly multifunctional intranuclear organelle in which, in addition to the canonical ribosome assembly, numerous processes such as transcription, DNA repair and replication, the cell cycle, and apoptosis are coordinated. The nucleolus is further a key hub in the sensing of cellular stress and undergoes major structural and compositional changes in response to cellular perturbations. Numerous nucleolar proteins have been identified that, upon sensing nucleolar stress, deploy additional, non-ribosomal roles in the regulation of varied cell processes including cell cycle arrest, arrest of DNA replication, induction of DNA repair, and apoptosis, among others. The highly abundant proteins nucleophosmin (NPM1) and nucleolin (NCL) are two such factors that transit to the nucleoplasm in response to stress, and participate directly in the repair of numerous different DNA damages. This review discusses the contributions made by NCL and (or) NPM1 to the different DNA repair pathways employed by mammalian cells to repair DNA insults, and examines the implications of such activities for the regulation, pathogenesis, and therapeutic targeting of NPM1 and NCL.
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Affiliation(s)
- Daniel D Scott
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
| | - Marlene Oeffinger
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
- c Département de biochimie et médecine moléculaire, Faculté de Médecine, Université de Montréal, QC H3T 1J4, Canada
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15
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Nicolas E, Parisot P, Pinto-Monteiro C, de Walque R, De Vleeschouwer C, Lafontaine DLJ. Involvement of human ribosomal proteins in nucleolar structure and p53-dependent nucleolar stress. Nat Commun 2016; 7:11390. [PMID: 27265389 PMCID: PMC4897761 DOI: 10.1038/ncomms11390] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 03/21/2016] [Indexed: 02/07/2023] Open
Abstract
The nucleolus is a potent disease biomarker and a target in cancer therapy. Ribosome biogenesis is initiated in the nucleolus where most ribosomal (r-) proteins assemble onto precursor rRNAs. Here we systematically investigate how depletion of each of the 80 human r-proteins affects nucleolar structure, pre-rRNA processing, mature rRNA accumulation and p53 steady-state level. We developed an image-processing programme for qualitative and quantitative discrimination of normal from altered nucleolar morphology. Remarkably, we find that uL5 (formerly RPL11) and uL18 (RPL5) are the strongest contributors to nucleolar integrity. Together with the 5S rRNA, they form the late-assembling central protuberance on mature 60S subunits, and act as an Hdm2 trap and p53 stabilizer. Other major contributors to p53 homeostasis are also strictly late-assembling large subunit r-proteins essential to nucleolar structure. The identification of the r-proteins that specifically contribute to maintaining nucleolar structure and p53 steady-state level provides insights into fundamental aspects of cell and cancer biology. The nucleolus is a specialized functional domain of the nucleus where ribosome biogenesis is initiated and also implicated in a p53-dependent anti-tumor surveillance. Here the authors use a quantitative imaging approach to detail the role of each ribosomal protein on the structural integrity of the nucleolus and p53 homeostasis.
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Affiliation(s)
- Emilien Nicolas
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium.,Center for Microscopy and Molecular Imaging, B-6041 Charleroi-Gosselies, Belgium
| | - Pascaline Parisot
- ICTEAM-ELEN, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Celina Pinto-Monteiro
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Roxane de Walque
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | | | - Denis L J Lafontaine
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium.,Center for Microscopy and Molecular Imaging, B-6041 Charleroi-Gosselies, Belgium
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16
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Caudron-Herger M, Pankert T, Seiler J, Németh A, Voit R, Grummt I, Rippe K. Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 2015; 34:2758-74. [PMID: 26464461 DOI: 10.15252/embj.201591458] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023] Open
Abstract
Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a functional link between aluRNA, nucleolus integrity and pre-rRNA synthesis. Furthermore, we show that aluRNAs interact with nucleolin and target ectopic genomic loci to the nucleolus. Our study suggests an aluRNA-based mechanism that links RNA polymerase I and II activities and modulates nucleolar structure and rRNA production.
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Affiliation(s)
- Maïwen Caudron-Herger
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Teresa Pankert
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Jeanette Seiler
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Attila Németh
- Department of Biochemistry III, Biochemistry Center Regensburg University of Regensburg, Regensburg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Karsten Rippe
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
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17
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Lafontaine DLJ. Noncoding RNAs in eukaryotic ribosome biogenesis and function. Nat Struct Mol Biol 2015; 22:11-9. [PMID: 25565028 DOI: 10.1038/nsmb.2939] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 11/26/2014] [Indexed: 12/22/2022]
Abstract
The ribosome, central to protein synthesis in all cells, is a complex multicomponent assembly with rRNA at its functional core. During the process of ribosome biogenesis, diverse noncoding RNAs participate in controlling the quantity and quality of this rRNA. In this Review, I discuss the multiple roles assumed by noncoding RNAs during the different steps of ribosome biogenesis and how they contribute to the generation of ribosome heterogeneity, which affects normal and pathophysiological processes.
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Affiliation(s)
- Denis L J Lafontaine
- RNA Molecular Biology, Fonds National de la Recherche Scientifique, Université Libre de Bruxelles, Brussels, Belgium
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18
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Stępiński D. Functional ultrastructure of the plant nucleolus. PROTOPLASMA 2014; 251:1285-306. [PMID: 24756369 PMCID: PMC4209244 DOI: 10.1007/s00709-014-0648-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 04/08/2014] [Indexed: 05/23/2023]
Abstract
Nucleoli are nuclear domains present in almost all eukaryotic cells. They not only specialize in the production of ribosomal subunits but also play roles in many fundamental cellular activities. Concerning ribosome biosynthesis, particular stages of this process, i.e., ribosomal DNA transcription, primary RNA transcript processing, and ribosome assembly proceed in precisely defined nucleolar subdomains. Although eukaryotic nucleoli are conservative in respect of their main function, clear morphological differences between these structures can be noticed between individual kingdoms. In most cases, a plant nucleolus shows well-ordered structure in which four main ultrastructural components can be distinguished: fibrillar centers, dense fibrillar component, granular component, and nucleolar vacuoles. Nucleolar chromatin is an additional crucial structural component of this organelle. Nucleolonema, although it is not always an unequivocally distinguished nucleolar domain, has often been described as a well-grounded morphological element, especially of plant nucleoli. The ratios and morphology of particular subcompartments of a nucleolus can change depending on its metabolic activity which in turn is correlated with the physiological state of a cell, cell type, cell cycle phase, as well as with environmental influence. Precise attribution of functions to particular nucleolar subregions in the process of ribosome biosynthesis is now possible using various approaches. The presented description of plant nucleolar morphology summarizes previous knowledge regarding the function of nucleoli as well as of their particular subdomains not only in the course of ribosome biosynthesis.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland,
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Louvet E, Yoshida A, Kumeta M, Takeyasu K. Probing the stiffness of isolated nucleoli by atomic force microscopy. Histochem Cell Biol 2014; 141:365-81. [PMID: 24297448 DOI: 10.1007/s00418-013-1167-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2013] [Indexed: 11/24/2022]
Abstract
In eukaryotic cells, ribosome biogenesis occurs in the nucleolus, a membraneless nuclear compartment. Noticeably, the nucleolus is also involved in several nuclear functions, such as cell cycle regulation, non-ribosomal ribonucleoprotein complex assembly, aggresome formation and some virus assembly. The most intriguing question about the nucleolus is how such dynamics processes can occur in such a compact compartment. We hypothesized that its structure may be rather flexible. To investigate this, we used atomic force microscopy (AFM) on isolated nucleoli. Surface topography imaging revealed the beaded structure of the nucleolar surface. With the AFM's ability to measure forces, we were able to determine the stiffness of isolated nucleoli. We could establish that the nucleolar stiffness varies upon drastic morphological changes induced by transcription and proteasome inhibition. Furthermore, upon ribosomal proteins and LaminB1 knockdowns, the nucleolar stiffness was increased. This led us to propose a model where the nucleolus has steady-state stiffness dependent on ribosome biogenesis activity and requires LaminB1 for its flexibility.
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Affiliation(s)
- Emilie Louvet
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan,
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20
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Abstract
As the most prominent sub-nuclear compartment in the interphase nucleus and the site of ribosome biogenesis, the nucleolus synthesizes and processes rRNA and also assembles ribosomal subunits. Though several lines of research in recent years have indicated that the nucleolus might have additional functions-such as the assembling of signal recognition particles, the processing of mRNA, tRNA and telomerase activities, and regulating the cell cycle-proteomic analyses of the nucleolus in three representative eukaryotic species has shown that a plethora of proteins either have no association with ribosome biogenesis or are of presently unknown function. This phenomenon further indicates that the composition and function of the nucleolus is far more complicated than previously thought. Meanwhile, the available nucleolar proteome databases has provided new approaches and led to remarkable progress in understanding the nucleolus. Here, we have summarized recent advances in the study of the nucleolus, including new discoveries of its structure, function, genomics/proteomics as well as its origin and evolution. Moreover, we highlight several of the important unresolved issues in this field.
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21
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Mapping the cleavage sites on mammalian pre-rRNAs: Where do we stand? Biochimie 2012; 94:1521-32. [DOI: 10.1016/j.biochi.2012.02.001] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 02/01/2012] [Indexed: 11/23/2022]
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