1
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Issa A, Schlotter F, Flayac J, Chen J, Wacheul L, Philippe M, Sardini L, Mostefa L, Vandermoere F, Bertrand E, Verheggen C, Lafontaine DL, Massenet S. The nucleolar phase of signal recognition particle assembly. Life Sci Alliance 2024; 7:e202402614. [PMID: 38858088 PMCID: PMC11165425 DOI: 10.26508/lsa.202402614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024] Open
Abstract
The signal recognition particle is essential for targeting transmembrane and secreted proteins to the endoplasmic reticulum. Remarkably, because they work together in the cytoplasm, the SRP and ribosomes are assembled in the same biomolecular condensate: the nucleolus. How important is the nucleolus for SRP assembly is not known. Using quantitative proteomics, we have investigated the interactomes of SRP components. We reveal that SRP proteins are associated with scores of nucleolar proteins important for ribosome biogenesis and nucleolar structure. Having monitored the subcellular distribution of SRP proteins upon controlled nucleolar disruption, we conclude that an intact organelle is required for their proper localization. Lastly, we have detected two SRP proteins in Cajal bodies, which indicates that previously undocumented steps of SRP assembly may occur in these bodies. This work highlights the importance of a structurally and functionally intact nucleolus for efficient SRP production and suggests that the biogenesis of SRP and ribosomes may be coordinated in the nucleolus by common assembly factors.
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Affiliation(s)
- Amani Issa
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Florence Schlotter
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Justine Flayac
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Jing Chen
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Ludivine Wacheul
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | | | - Lucas Sardini
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Lalia Mostefa
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
| | | | | | | | - Denis Lj Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Séverine Massenet
- https://ror.org/04vfs2w97 Université de Lorraine, CNRS, IMoPA, Nancy, France
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2
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Model MA, Guo R, Fasina K, Jin R, Clements RJ, Leff LG. Measurement of protein concentration in bacteria and small organelles under a light transmission microscope. J Mol Recognit 2024:e3099. [PMID: 38923720 DOI: 10.1002/jmr.3099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/25/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
Protein concentration (PC) is an essential characteristic of cells and organelles; it determines the extent of macromolecular crowding effects and serves as a sensitive indicator of cellular health. A simple and direct way to quantify PC is provided by brightfield-based transport-of-intensity equation (TIE) imaging combined with volume measurements. However, since TIE is based on geometric optics, its applicability to micrometer-sized particles is not clear. Here, we show that TIE can be used on particles with sizes comparable to the wavelength. At the same time, we introduce a new ImageJ plugin that allows TIE image processing without resorting to advanced mathematical programs. To convert TIE data to PC, knowledge of particle volumes is essential. The volumes of bacteria or other isolated particles can be measured by displacement of an external absorbing dye ("transmission-through-dye" or TTD microscopy), and for spherical intracellular particles, volumes can be estimated from their diameters. We illustrate the use of TIE on Escherichia coli, mammalian nucleoli, and nucleolar fibrillar centers. The method is easy to use and achieves high spatial resolution.
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Affiliation(s)
- M A Model
- Department of Biological Science, Kent State University, Kent, Ohio, USA
| | - R Guo
- Department of Computer Science, Kent State University, Kent, Ohio, USA
| | - K Fasina
- Department of Biological Science, Kent State University, Kent, Ohio, USA
| | - R Jin
- Department of Computer Science, Kent State University, Kent, Ohio, USA
| | - R J Clements
- Department of Biological Science, Kent State University, Kent, Ohio, USA
| | - L G Leff
- Department of Biological Science, Kent State University, Kent, Ohio, USA
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3
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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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4
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Zorbas C, Soenmez A, Léger J, De Vleeschouwer C, Lafontaine DL. Detecting material state changes in the nucleolus by label-free digital holographic microscopy. EMBO Rep 2024; 25:2786-2811. [PMID: 38654122 PMCID: PMC11169520 DOI: 10.1038/s44319-024-00134-5] [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: 03/15/2023] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Ribosome biogenesis is initiated in the nucleolus, a multiphase biomolecular condensate formed by liquid-liquid phase separation. The nucleolus is a powerful disease biomarker and stress biosensor whose morphology reflects function. Here we have used digital holographic microscopy (DHM), a label-free quantitative phase contrast microscopy technique, to detect nucleoli in adherent and suspension human cells. We trained convolutional neural networks to detect and quantify nucleoli automatically on DHM images. Holograms containing cell optical thickness information allowed us to define a novel index which we used to distinguish nucleoli whose material state had been modulated optogenetically by blue-light-induced protein aggregation. Nucleoli whose function had been impacted by drug treatment or depletion of ribosomal proteins could also be distinguished. We explored the potential of the technology to detect other natural and pathological condensates, such as those formed upon overexpression of a mutant form of huntingtin, ataxin-3, or TDP-43, and also other cell assemblies (lipid droplets). We conclude that DHM is a powerful tool for quantitatively characterizing nucleoli and other cell assemblies, including their material state, without any staining.
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Affiliation(s)
- Christiane Zorbas
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041, Gosselies, Belgium
| | - Aynur Soenmez
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041, Gosselies, Belgium
| | - Jean Léger
- ICTEAM-ELEN, Fonds de la Recherche Scientifique (F.R.S./FNRS), UCLouvain, B-1348, Louvain-la-Neuve, Belgium
| | - Christophe De Vleeschouwer
- ICTEAM-ELEN, Fonds de la Recherche Scientifique (F.R.S./FNRS), UCLouvain, B-1348, Louvain-la-Neuve, Belgium
| | - Denis Lj Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041, Gosselies, Belgium.
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5
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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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6
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Tan T, Gao B, Yu H, Pan H, Sun Z, Lei A, Zhang L, Lu H, Wu H, Daley GQ, Feng Y, Zhang J. Dynamic nucleolar phase separation influenced by non-canonical function of LIN28A instructs pluripotent stem cell fate decisions. Nat Commun 2024; 15:1256. [PMID: 38341436 PMCID: PMC10858886 DOI: 10.1038/s41467-024-45451-4] [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: 02/23/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
LIN28A is important in somatic reprogramming and pluripotency regulation. Although previous studies addressed that LIN28A can repress let-7 microRNA maturation in the cytoplasm, few focused on its role within the nucleus. Here, we show that the nucleolus-localized LIN28A protein undergoes liquid-liquid phase separation (LLPS) in mouse embryonic stem cells (mESCs) and in vitro. The RNA binding domains (RBD) and intrinsically disordered regions (IDR) of LIN28A contribute to LIN28A and the other nucleolar proteins' phase-separated condensate establishment. S120A, S200A and R192G mutations in the IDR result in subcellular mislocalization of LIN28A and abnormal nucleolar phase separation. Moreover, we find that the naive-to-primed pluripotency state conversion and the reprogramming are associated with dynamic nucleolar remodeling, which depends on LIN28A's phase separation capacity, because the LIN28A IDR point mutations abolish its role in regulating nucleolus and in these cell fate decision processes, and an exogenous IDR rescues it. These findings shed light on the nucleolar function in pluripotent stem cell states and on a non-canonical RNA-independent role of LIN28A in phase separation and cell fate decisions.
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Affiliation(s)
- Tianyu Tan
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 310000, China
| | - Bo Gao
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hua Yu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Hongru Pan
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Zhen Sun
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Anhua Lei
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Li Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Hengxing Lu
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 310000, China
| | - Hao Wu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - George Q Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Jin Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 310000, China.
- Institute of Hematology, Zhejiang University, Hangzhou, 310058, China.
- Center of Gene/Cell Engineering and Genome Medicine, Hangzhou, 310058, China.
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7
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Ogienko AA, Korepina MO, Pindyurin AV, Omelina ES. New Functional Motifs for the Targeted Localization of Proteins to the Nucleolus in Drosophila and Human Cells. Int J Mol Sci 2024; 25:1230. [PMID: 38279227 PMCID: PMC10817092 DOI: 10.3390/ijms25021230] [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: 12/14/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
The nucleolus is a significant nuclear organelle that is primarily known for its role in ribosome biogenesis. However, emerging evidence suggests that the nucleolus may have additional functions. Particularly, it is involved in the organization of the three-dimensional structure of the genome. The nucleolus acts as a platform for the clustering of repressed chromatin, although this process is not yet fully understood, especially in the context of Drosophila. One way to study the regions of the genome that cluster near the nucleolus in Drosophila demands the identification of a reliable nucleolus-localizing signal (NoLS) motif(s) that can highly specifically recruit the protein of interest to the nucleolus. Here, we tested a series of various NoLS motifs from proteins of different species, as well as some of their combinations, for the ability to drive the nucleolar localization of the chimeric H2B-GFP protein. Several short motifs were found to effectively localize the H2B-GFP protein to the nucleolus in over 40% of transfected Drosophila S2 cells. Furthermore, it was demonstrated that NoLS motifs derived from Drosophila proteins exhibited greater efficiency compared to that of those from other species.
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Affiliation(s)
- Anna A. Ogienko
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
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8
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Zhou L, Wang S, Hu W, Liu X, Xu L, Tong B, Zhang T, Xue Z, Guo Y, Zhao J, Lu L, Fan H, Qian W, Chen J, Chen W, Wang L. T cell proliferation requires ribosomal maturation in nucleolar condensates dependent on DCAF13. J Cell Biol 2023; 222:e202201096. [PMID: 37615668 PMCID: PMC10450623 DOI: 10.1083/jcb.202201096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/16/2023] [Accepted: 07/31/2023] [Indexed: 08/25/2023] Open
Abstract
T cells require rapid proliferation to initiate adaptive immunity to prevent pathogen attacks. The nucleolus, a distinct subnuclear membrane-less compartment for ribosomal biogenesis, is indispensable for cell proliferation. However, specific nucleolar proteins involved in rapid T cell proliferation and their underlying molecular regulatory mechanism remain elusive. Here, we identified an essential nucleolar protein, DCAF13, in T cells and revealed its significant regulation of rapid T cell proliferation. Its depletion drastically impairs T cell proliferation due to severe 18S rRNA maturation failure, consequent abnormal ribosome assembly in nucleoli, and insufficient production of nascent proteins. Mechanistically, we propose that DCAF13 promotes NPM1 phase separation to accelerate pre-RNA enrichment and its endonuclease UTP23 for 18S rRNA maturation during T cell proliferation. Our findings reveal the modulatory effect of nucleolar NPM1/DCAF13 phase separation on ribosomal maturation to ensure rapid T cell proliferation and further pathogen clearance for the first time.
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Affiliation(s)
- Lina Zhou
- Bone Marrow Transplantation Center and Institute of Immunology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Shuai Wang
- Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Hu
- Zhejiang University School of Medicine, Hangzhou, China
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqian Liu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Lingdong Xu
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
| | - Bolu Tong
- Zhejiang University School of Medicine, Hangzhou, China
| | - Tongtong Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Center for Integrated Oncology and Precision Medicine, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhonghui Xue
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yixin Guo
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Haining, China
| | - Jing Zhao
- Department of Pathology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Linrong Lu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Hengyu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Wenbin Qian
- Department of Hematology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Chen
- Department of General Surgery of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wei Chen
- Zhejiang University School of Medicine, Hangzhou, China
- Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Lie Wang
- Bone Marrow Transplantation Center and Institute of Immunology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
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9
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Sheu-Gruttadauria J, Yan X, Stuurman N, Floor SN, Vale RD. Nucleolar dynamics are determined by the ordered assembly of the ribosome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559432. [PMID: 37808656 PMCID: PMC10557630 DOI: 10.1101/2023.09.26.559432] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Ribosome biogenesis is coordinated within the nucleolus, a biomolecular condensate that exhibits dynamic material properties that are thought to be important for nucleolar function. However, the relationship between ribosome assembly and nucleolar dynamics is not clear. Here, we screened 364 genes involved in ribosome biogenesis and RNA metabolism for their impact on dynamics of the nucleolus, as measured by automated, high-throughput fluorescence recovery after photobleaching (FRAP) of the nucleolar scaffold protein NPM1. This screen revealed that gene knockdowns that caused accumulation of early rRNA intermediates were associated with nucleolar rigidification, while accumulation of late intermediates led to increased fluidity. These shifts in dynamics were accompanied by distinct changes in nucleolar morphology. We also found that genes involved in mRNA processing impact nucleolar dynamics, revealing connections between ribosome biogenesis and other RNA processing pathways. Together, this work defines mechanistic ties between ribosome assembly and the biophysical features of the nucleolus, while establishing a toolbox for understanding how molecular dynamics impact function across other biomolecular condensates.
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Affiliation(s)
- Jessica Sheu-Gruttadauria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Xiaowei Yan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Present address: Department of Dermatology, Stanford, CA, USA
| | - Nico Stuurman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Present address: Altos Labs, Redwood City, CA, USA
| | - Stephen N. Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Ronald D. Vale
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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10
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Montacié C, Riondet C, Wei L, Darrière T, Weiss A, Pontvianne F, Escande ML, de Bures A, Jobet E, Barbarossa A, Carpentier MC, Aarts MGM, Attina A, Hirtz C, David A, Marchand V, Motorin Y, Curie C, Mari S, Reichheld JP, Sáez-Vásquez J. NICOTIANAMINE SYNTHASE activity affects nucleolar iron accumulation and impacts rDNA silencing and RNA methylation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4384-4400. [PMID: 37179467 PMCID: PMC10433931 DOI: 10.1093/jxb/erad180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/11/2023] [Indexed: 05/15/2023]
Abstract
In plant cells, a large pool of iron (Fe) is contained in the nucleolus, as well as in chloroplasts and mitochondria. A central determinant for intracellular distribution of Fe is nicotianamine (NA) generated by NICOTIANAMINE SYNTHASE (NAS). Here, we used Arabidopsis thaliana plants with disrupted NAS genes to study the accumulation of nucleolar iron and understand its role in nucleolar functions and more specifically in rRNA gene expression. We found that nas124 triple mutant plants, which contained lower quantities of the iron ligand NA, also contained less iron in the nucleolus. This was concurrent with the expression of normally silenced rRNA genes from nucleolar organizer regions 2 (NOR2). Notably, in nas234 triple mutant plants, which also contained lower quantities of NA, nucleolar iron and rDNA expression were not affected. In contrast, in both nas124 and nas234, specific RNA modifications were differentially regulated in a genotype dependent manner. Taken together, our results highlight the impact of specific NAS activities in RNA gene expression. We discuss the interplay between NA and nucleolar iron with rDNA functional organization and RNA methylation.
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Affiliation(s)
- Charlotte Montacié
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Christophe Riondet
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Lili Wei
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Tommy Darrière
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Alizée Weiss
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Frédéric Pontvianne
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Line Escande
- Observatoire Océanologique de Banyuls s/ mer, CNRS, 66650 Banyuls-sur-mer, France
- BioPIC Platform of the OOB, 66650 Banyuls-sur-mer, France
| | - Anne de Bures
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Edouard Jobet
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Adrien Barbarossa
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, 6700AA Wageningen, Netherlands
| | - Aurore Attina
- INSERM, CHU Montpellier, CNRS, IRMB, Université Montpellier, 34090Montpellier, France
| | - Christophe Hirtz
- INSERM, CHU Montpellier, CNRS, IRMB, Université Montpellier, 34090Montpellier, France
| | - Alexandre David
- IGF, CNRS, INSERM, Université Montpellier, 34090Montpellier, France
| | - Virginie Marchand
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, CNRS, INSERM, IBSLor (UMS2008/US40), Université de Lorraine, F-54000 Nancy, France
| | - Yuri Motorin
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, CNRS, INSERM, IBSLor (UMS2008/US40), Université de Lorraine, F-54000 Nancy, France
- CNRS, IMoPA (UMR 7365), Université de Lorraine, F-54000 Nancy, France
| | - Catherine Curie
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Stéphane Mari
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Julio Sáez-Vásquez
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
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11
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Dash S, Lamb MC, Lange JJ, McKinney MC, Tsuchiya D, Guo F, Zhao X, Corbin TJ, Kirkman M, Delventhal K, Moore EL, McKinney S, Shiang R, Trainor PA. rRNA transcription is integral to phase separation and maintenance of nucleolar structure. PLoS Genet 2023; 19:e1010854. [PMID: 37639467 PMCID: PMC10513380 DOI: 10.1371/journal.pgen.1010854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/21/2023] [Accepted: 07/03/2023] [Indexed: 08/31/2023] Open
Abstract
Transcription of ribosomal RNA (rRNA) by RNA Polymerase (Pol) I in the nucleolus is necessary for ribosome biogenesis, which is intimately tied to cell growth and proliferation. Perturbation of ribosome biogenesis results in tissue specific disorders termed ribosomopathies in association with alterations in nucleolar structure. However, how rRNA transcription and ribosome biogenesis regulate nucleolar structure during normal development and in the pathogenesis of disease remains poorly understood. Here we show that homozygous null mutations in Pol I subunits required for rRNA transcription and ribosome biogenesis lead to preimplantation lethality. Moreover, we discovered that Polr1a-/-, Polr1b-/-, Polr1c-/- and Polr1d-/- mutants exhibit defects in the structure of their nucleoli, as evidenced by a decrease in number of nucleolar precursor bodies and a concomitant increase in nucleolar volume, which results in a single condensed nucleolus. Pharmacological inhibition of Pol I in preimplantation and midgestation embryos, as well as in hiPSCs, similarly results in a single condensed nucleolus or fragmented nucleoli. We find that when Pol I function and rRNA transcription is inhibited, the viscosity of the granular compartment of the nucleolus increases, which disrupts its phase separation properties, leading to a single condensed nucleolus. However, if a cell progresses through mitosis, the absence of rRNA transcription prevents reassembly of the nucleolus and manifests as fragmented nucleoli. Taken together, our data suggests that Pol I function and rRNA transcription are required for maintaining nucleolar structure and integrity during development and in the pathogenesis of disease.
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Affiliation(s)
- Soma Dash
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Maureen C. Lamb
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Mary C. McKinney
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Fengli Guo
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Xia Zhao
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Timothy J. Corbin
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - MaryEllen Kirkman
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Kym Delventhal
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Emma L. Moore
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Rita Shiang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
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12
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Lafontaine DLJ. In phase with the nucleolus. Cell Res 2023; 33:579-580. [PMID: 37055593 PMCID: PMC10397221 DOI: 10.1038/s41422-023-00801-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Affiliation(s)
- Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark Campus, B-6041, Gosselies, Belgium.
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13
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Zhang R, Shokri-Kojori E, Volkow ND. Seasonal effect-an overlooked factor in neuroimaging research. Transl Psychiatry 2023; 13:238. [PMID: 37400428 DOI: 10.1038/s41398-023-02530-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023] Open
Abstract
In neuroimaging research, seasonal effects are often neglected or controlled as confounding factors. However, seasonal fluctuations in mood and behavior have been observed in both psychiatric disorders and healthy participants. There are vast opportunities for neuroimaging studies to understand seasonal variations in brain function. In this study, we used two longitudinal single-subject datasets with weekly measures over more than a year to investigate seasonal effects on intrinsic brain networks. We found that the sensorimotor network displayed a strong seasonal pattern. The sensorimotor network is not only relevant for integrating sensory inputs and coordinating movement, but it also affects emotion regulation and executive function. Therefore, the observed seasonality effects in the sensorimotor network could contribute to seasonal variations in mood and behavior. Genetic analyses revealed seasonal modulation of biological processes and pathways relevant to immune function, RNA metabolism, centrosome separation, and mitochondrial translation that have a significant impact on human physiology and pathology. In addition, we revealed critical factors such as head motion, caffeine use, and scan time that could interfere with seasonal effects and need to be considered in future studies.
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Affiliation(s)
- Rui Zhang
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892-1013, USA.
| | - Ehsan Shokri-Kojori
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892-1013, USA
| | - Nora D Volkow
- Laboratory of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892-1013, USA.
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14
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Wu S, Chen J, Teo BHD, Wee SYK, Wong MHM, Cui J, Chen J, Leong KP, Lu J. The axis of complement C1 and nucleolus in antinuclear autoimmunity. Front Immunol 2023; 14:1196544. [PMID: 37359557 PMCID: PMC10288996 DOI: 10.3389/fimmu.2023.1196544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Antinuclear autoantibodies (ANA) are heterogeneous self-reactive antibodies that target the chromatin network, the speckled, the nucleoli, and other nuclear regions. The immunological aberration for ANA production remains partially understood, but ANA are known to be pathogenic, especially, in systemic lupus erythematosus (SLE). Most SLE patients exhibit a highly polygenic disease involving multiple organs, but in rare complement C1q, C1r, or C1s deficiencies, the disease can become largely monogenic. Increasing evidence point to intrinsic autoimmunogenicity of the nuclei. Necrotic cells release fragmented chromatins as nucleosomes and the alarmin HMGB1 is associated with the nucleosomes to activate TLRs and confer anti-chromatin autoimmunogenecity. In speckled regions, the major ANA targets Sm/RNP and SSA/Ro contain snRNAs that confer autoimmunogenecity to Sm/RNP and SSA/Ro antigens. Recently, three GAR/RGG-containing alarmins have been identified in the nucleolus that helps explain its high autoimmunogenicity. Interestingly, C1q binds to the nucleoli exposed by necrotic cells to cause protease C1r and C1s activation. C1s cleaves HMGB1 to inactive its alarmin activity. C1 proteases also degrade many nucleolar autoantigens including nucleolin, a major GAR/RGG-containing autoantigen and alarmin. It appears that the different nuclear regions are intrinsically autoimmunogenic by containing autoantigens and alarmins. However, the extracellular complement C1 complex function to dampen nuclear autoimmunogenecity by degrading these nuclear proteins.
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Affiliation(s)
- Shan Wu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Junjie Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Boon Heng Dennis Teo
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Seng Yin Kelly Wee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ming Hui Millie Wong
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jianzhou Cui
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jinmiao Chen
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Khai Pang Leong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Jinhua Lu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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15
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Lin L, Bao Z, Jiang P, Xu Z, Shi B, Xu G, Wang D, Wei X, Gu B. Superior biocompatible carbon dots for dynamic fluorescence imaging of nucleoli in living cells. Biomater Sci 2023; 11:2935-2949. [PMID: 36912088 DOI: 10.1039/d2bm02139k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The nucleolus is a newly developed and promising target for cancer diagnosis and therapy, and its imaging is extremely significant for fundamental research and clinical applications. The unique feature, i.e., high resolution at the subcellular level, makes the fluorescence imaging method a powerful tool for nucleolus imaging. However, the fluorescence imaging of nucleoli in living cells is restricted by the limited availability of fluorescent agents with specific nucleolus-targeting capability and superior biocompatibility. Here, promising carbon dots (CDs) with intrinsic nucleolus-targeting capability were synthesized, characterized and employed for dynamic fluorescence imaging of nucleoli in living cells. The CDs exhibit a high fluorescence quantum yield of 0.2, excellent specificity and photostability, and superior biocompatibility, which were systematically demonstrated at the gene, cellular and animal levels and confirmed by their biological effects on embryonic development. All these features enabled CDs to light up the nucleoli for a long time with a high signal-to-noise ratio in living cells and monitor the nucleolar dynamics of malignant cells in camptothecin (CPT) based chemotherapy. Their excellent optical and biological features as well as general nucleolus-targeting capability endow CDs with great potential for future translational research.
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Affiliation(s)
- Liyun Lin
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Zhouzhou Bao
- Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pengfei Jiang
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Zhourui Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518055, China.
| | - Bo Shi
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Gaixia Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518055, China.
| | - Dan Wang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Xunbin Wei
- Biomedical Engineering Department and International Cancer Institute, Peking University, Beijing 100081, China.
| | - Bobo Gu
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China.
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16
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Girke P, Seufert W. Targeting of Hmo1 to subcompartments of the budding yeast nucleolus. Mol Biol Cell 2023; 34:ar22. [PMID: 36696177 PMCID: PMC10011721 DOI: 10.1091/mbc.e22-07-0261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The nucleolus is a multilayered, membraneless organelle made up of liquidlike biogenesis compartments surrounding an array of ribosomal RNA genes (rDNA). Biogenesis factors accumulate in the outer compartments through RNA binding and phase separation promoted by intrinsically disordered protein regions. In contrast, the nucleolar localization of rDNA-binding proteins, which reside in the central chromatin compartment, is less well characterized. To gain mechanistic insight, we analyzed the localization, mitotic segregation, nucleic acid binding, and nuclear dynamics of the budding yeast rDNA-binding protein Hmo1. Deletion of the main DNA-binding domain, the HMG boxB, compromised Hmo1 transfer to daughter cells in mitosis and transcription-independent rDNA association but still allowed nucleolar localization. The C-terminal lysine-rich region turned out to be a combined nuclear and nucleolar localization sequence (NLS-NoLS). Its integrity was required for maximal enrichment and efficient retention of Hmo1 in the nucleolus and nucleolar localization of the ΔboxB construct. Moreover, the NLS-NoLS region was sufficient to promote nucleolar accumulation and bound nucleic acids in vitro with some preference for RNA. Bleaching experiments indicated mobility of Hmo1 inside the nucleolus but little exchange with the nucleoplasm. Thus, a bilayered targeting mechanism secures proper localization of Hmo1 to the nucleolus.
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Affiliation(s)
- Philipp Girke
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
| | - Wolfgang Seufert
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
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17
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Chromatin localization of nucleophosmin organizes ribosome biogenesis. Mol Cell 2022; 82:4443-4457.e9. [PMID: 36423630 PMCID: PMC9949351 DOI: 10.1016/j.molcel.2022.10.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 11/24/2022]
Abstract
Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin compartment and move to the outer granular component, where maturation occurs. We find that the Schizosaccharomyces pombe nucleophosmin-like protein Fkbp39 localizes to rDNA sites encoding the 60S subunit rRNA, and this localization contributes to its specific association with nascent 60S subunits. Fkbp39 dissociates from chromatin to bind nascent 60S subunits, causing the latter to partition away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. In vivo, Fkbp39 binding directs the translocation of nascent 60S subunits toward the nucleophosmin-rich granular component. This process increases the efficiency of 60S subunit assembly, facilitating the incorporation of 60S RNA domain III. Thus, chromatin localization determines the specificity of nucleophosmin in sorting nascent ribosomal subunits and coordinates their movement into specialized assembly compartments within the nucleolus.
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18
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Identification of Novel mRNA Isoforms Associated with Acute Heat Stress Response Using RNA Sequencing Data in Sprague Dawley Rats. BIOLOGY 2022; 11:biology11121740. [PMID: 36552250 PMCID: PMC9774719 DOI: 10.3390/biology11121740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022]
Abstract
The molecular mechanisms underlying heat stress tolerance in animals to high temperatures remain unclear. This study identified the differentially expressed mRNA isoforms which narrowed down the most reliable DEG markers and molecular pathways that underlie the mechanisms of thermoregulation. This experiment was performed on Sprague Dawley rats housed at 22 °C (control group; CT), and three acute heat-stressed groups housed at 42 °C for 30 min (H30), 60 min (H60), and 120 min (H120). Earlier, we demonstrated that acute heat stress increased the rectal temperature of rats, caused abnormal changes in the blood biochemical parameters, as well as induced dramatic changes in the expression levels of genes through epigenetics and post-transcriptional regulation. Transcriptomic analysis using RNA-Sequencing (RNA-Seq) data obtained previously from blood (CT and H120), liver (CT, H30, H60, and H120), and adrenal glands (CT, H30, H60, and H120) was performed. The differentially expressed mRNA isoforms (DEIs) were identified and annotated by the CLC Genomics Workbench. Biological process and metabolic pathway analyses were performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 225, 5764, and 4988 DEIs in the blood, liver, and adrenal glands were observed. Furthermore, the number of novel differentially expressed transcript lengths with annotated genes and novel differentially expressed transcript with non-annotated genes were 136 and 8 in blood, 3549 and 120 in the liver, as well as 3078 and 220 in adrenal glands, respectively. About 35 genes were involved in the heat stress response, out of which, Dnaja1, LOC680121, Chordc1, AABR07011951.1, Hsp90aa1, Hspa1b, Cdkn1a, Hmox1, Bag3, and Dnaja4 were commonly identified in the liver and adrenal glands, suggesting that these genes may regulate heat stress response through interactions between the liver and adrenal glands. In conclusion, this study would enhance our understanding of the complex underlying mechanisms of acute heat stress, and the identified mRNA isoforms and genes can be used as potential candidates for thermotolerance selection in mammals.
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19
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Heng H, Liu J, Hu M, Li D, Su W, Li J. WDR43 is a potential diagnostic biomarker and therapeutic target for osteoarthritis complicated with Parkinson’s disease. Front Cell Neurosci 2022; 16:1013745. [DOI: 10.3389/fncel.2022.1013745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Osteoarthritis (OA) and Parkinson’s disease (PD) are on the rise and greatly impact the quality of individuals’ lives. Although accumulating evidence indicates a relationship between OA and PD, the particular interactions connecting the two diseases have not been thoroughly examined. Therefore, this study explored the association through genetic characterization and functional enrichment. Four datasets (GSE55235, GSE12021, GSE7621, and GSE42966) were chosen for assessment and validation from the Gene Expression Omnibus (GEO) database. Weighted Gene Co-Expression Network Analysis (WGCNA) was implemented to determine the most relevant genes for clinical features. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were carried out to explore the biological processes of common genes, and to display the interrelationships between common genes, the STRING database and the application Molecular Complex Detection Algorithm (MCODE) of Cytoscape software were leveraged to get hub genes. By intersecting the common genes with the differentially expressed genes (DEGs) acquired from GSE12021 and GSE42966, the hub genes were identified. Finally, we validated the diagnostic efficacy of hub genes and explored their correlation with 22 immune infiltrating cells. As a consequence, we discovered 71 common genes, most of which were functionally enriched in antigen processing and presentation, mitochondrial translation, the mRNA surveillance pathway, and nucleocytoplasmic transport. Furthermore, WDR43 was found by intersecting eight hub genes with 28 DEGs from the two validation datasets. Receiver Operating Characteristic (ROC) implied the diagnostic role of WDR43 in OA and PD. Immune infiltration research revealed that T-cell regulatory (Tregs), monocytes, and mast cells resting were associated with the pathogenesis of OA and PD. WDR43 may provide key insights into the relationship between OA and PD.
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20
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Liu S, Zhang Q, He H, Yi M, Tan W, Guo J, Xu B. Intranuclear Nanoribbons for Selective Killing of Osteosarcoma Cells. Angew Chem Int Ed Engl 2022; 61:e202210568. [PMID: 36102872 PMCID: PMC9869109 DOI: 10.1002/anie.202210568] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 01/26/2023]
Abstract
Herein, we show intranuclear nanoribbons formed upon dephosphorylation of leucine-rich L- or D-phosphopeptide catalyzed by alkaline phosphatase (ALP) to selectively kill osteosarcoma cells. Being dephosphorylated by ALP, the peptides are first transformed into micelles and then converted into nanoribbons. The peptides/assemblies first aggregate on cell membranes, then enter cells via endocytosis, and finally accumulate in nuclei (mainly in nucleoli). Proteomics analysis suggests that the assemblies interact with histone proteins. The peptides kill osteosarcoma cells rapidly and are nontoxic to normal cells. Moreover, the repeated stimulation of the osteosarcoma cells by the peptides sensitizes the cancer cells rather than inducing resistance. This work not only illustrates a novel mechanism for nucleus targeting, but may also pave a new way for selectively killing osteosarcoma cells and minimizing drug resistance.
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Affiliation(s)
- Shuang Liu
- School of Materials Science and Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan, Hubei, 430070, China
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Qiuxin Zhang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
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21
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Yan D, Hua L. Nucleolar stress: Friend or foe in cardiac function? Front Cardiovasc Med 2022; 9:1045455. [PMID: 36386352 PMCID: PMC9659567 DOI: 10.3389/fcvm.2022.1045455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/17/2022] [Indexed: 03/14/2024] Open
Abstract
Studies in the past decades have uncovered an emerging role of the nucleolus in stress response and human disease progression. The disruption of ribosome biogenesis in the nucleolus causes aberrant nucleolar architecture and function, termed nucleolar stress, to initiate stress-responsive pathways via nucleolar release sequestration of various proteins. While data obtained from both clinical and basic investigations have faithfully demonstrated an involvement of nucleolar stress in the pathogenesis of cardiomyopathy, much remains unclear regarding its precise role in the progression of cardiac diseases. On the one hand, the initiation of nucleolar stress following acute myocardial damage leads to the upregulation of various cardioprotective nucleolar proteins, including nucleostemin (NS), nucleophosmin (NPM) and nucleolin (NCL). As a result, nucleolar stress plays an important role in facilitating the survival and repair of cardiomyocytes. On the other hand, abnormalities in nucleolar architecture and function are correlated with the deterioration of cardiac diseases. Notably, the cardiomyocytes of advanced ischemic and dilated cardiomyopathy display impaired silver-stained nucleolar organiser regions (AgNORs) and enlarged nucleoli, resembling the characteristics of tissue aging. Collectively, nucleolar abnormalities are critically involved in the development of cardiac diseases.
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Affiliation(s)
- Daliang Yan
- Department of Cardiovascular Surgery, Taizhou People’s Hospital, Taizhou, China
| | - Lu Hua
- Department of Oncology, Taizhou People’s Hospital, Taizhou, China
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22
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Mohapatra P, Mohanty S, Ansari SA, Shriwas O, Ghosh A, Rath R, Majumdar SKD, Swain RK, Raghav SK, Dash R. CMTM6 attenuates cisplatin-induced cell death in OSCC by regulating AKT/c-Myc-driven ribosome biogenesis. FASEB J 2022; 36:e22566. [PMID: 36165231 DOI: 10.1096/fj.202200808rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 11/11/2022]
Abstract
CMTM6, a type 3 transmembrane protein, is known to stabilize the expression of programmed cell death ligand 1 (PD-L1) and hence facilitates the immune evasion of tumor cells. Recently, we demonstrated that CMTM6 is a major driver of cisplatin resistance in oral squamous cell carcinomas (OSCC). However, the detailed mechanism of how CMTM6 rewires cisplatin resistance in OSCC is yet to be explored. RNA sequencing analysis of cisplatin-resistant OSCC lines stably expressing Nt shRNA and CMTM6 shRNA revealed that CMTM6 might be a potential regulator of the ribosome biogenesis network. Knocking down CMTM6 significantly inhibited transcription of 47S precursor rRNA and hindered the nucleolar structure, indicating reduced ribosome biogenesis. When CMTM6 was ectopically over-expressed in CMTM6KD cells, almost all ribosomal machinery components were rescued. Mechanistically, CMTM6 induced the expression of C-Myc, which promotes RNA polymerase I mediated rDNA transcription. In addition to this, CMTM6 was also found to regulate the AKT-mTORC1-dependent ribosome biogenesis and protein synthesis in cisplatin-resistant lines. The nude mice and zebrafish xenograft experiments indicate that blocking ribosome synthesis either by genetic inhibitor (CMTM6KD) or pharmacological inhibitor (CX-5461) significantly restores cisplatin-mediated cell death in chemoresistant OSCC. Overall, our study suggests that CMTM6 is a major regulator of the ribosome biogenesis network and targeting the ribosome biogenesis network is a viable target to overcome chemoresistance in OSCC. The novel combination of CX-5461 and cisplatin deserves further clinical investigation in advanced OSCC.
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Affiliation(s)
- Pallavi Mohapatra
- Cancer biology Unit, Institute of Life Sciences, Bhubaneswar, India.,Regional Centre for Biotechnology, Faridabad, India
| | - Sibasish Mohanty
- Cancer biology Unit, Institute of Life Sciences, Bhubaneswar, India.,Regional Centre for Biotechnology, Faridabad, India
| | - Shamima Azma Ansari
- Cancer biology Unit, Institute of Life Sciences, Bhubaneswar, India.,Regional Centre for Biotechnology, Faridabad, India
| | | | - Arup Ghosh
- Cancer biology Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Rachna Rath
- Sriram Chandra Bhanj Dental College and Hospital, Cuttack, India
| | | | - Rajeeb K Swain
- Cancer biology Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Sunil K Raghav
- Cancer biology Unit, Institute of Life Sciences, Bhubaneswar, India.,Regional Centre for Biotechnology, Faridabad, India.,Manipal Academy of Higher Education, Manipal, India
| | - Rupesh Dash
- Cancer biology Unit, Institute of Life Sciences, Bhubaneswar, India
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23
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Lacroix E, Audas TE. Keeping up with the condensates: The retention, gain, and loss of nuclear membrane-less organelles. Front Mol Biosci 2022; 9:998363. [PMID: 36203874 PMCID: PMC9530788 DOI: 10.3389/fmolb.2022.998363] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/19/2022] [Indexed: 12/04/2022] Open
Abstract
In recent decades, a growing number of biomolecular condensates have been identified in eukaryotic cells. These structures form through phase separation and have been linked to a diverse array of cellular processes. While a checklist of established membrane-bound organelles is present across the eukaryotic domain, less is known about the conservation of membrane-less subcellular structures. Many of these structures can be seen throughout eukaryotes, while others are only thought to be present in metazoans or a limited subset of species. In particular, the nucleus is a hub of biomolecular condensates. Some of these subnuclear domains have been found in a broad range of organisms, which is a characteristic often attributed to essential functionality. However, this does not always appear to be the case. For example, the nucleolus is critical for ribosomal biogenesis and is present throughout the eukaryotic domain, while the Cajal bodies are believed to be similarly conserved, yet these structures are dispensable for organismal survival. Likewise, depletion of the Drosophila melanogaster omega speckles reduces viability, despite the apparent absence of this domain in higher eukaryotes. By reviewing primary research that has analyzed the presence of specific condensates (nucleoli, Cajal bodies, amyloid bodies, nucleolar aggresomes, nuclear speckles, nuclear paraspeckles, nuclear stress bodies, PML bodies, omega speckles, NUN bodies, mei2 dots) in a cross-section of organisms (e.g., human, mouse, D. melanogaster, Caenorhabditis elegans, yeast), we adopt a human-centric view to explore the emergence, retention, and absence of a subset of nuclear biomolecular condensates. This overview is particularly important as numerous biomolecular condensates have been linked to human disease, and their presence in additional species could unlock new and well characterized model systems for health research.
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Affiliation(s)
- Emma Lacroix
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Timothy E. Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada
- *Correspondence: Timothy E. Audas,
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24
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Wittmeier A, Bernhardt M, Robisch AL, Cassini C, Osterhoff M, Salditt T, Köster S. Combined optical fluorescence microscopy and X-ray tomography reveals substructures in cell nuclei in 3D. BIOMEDICAL OPTICS EXPRESS 2022; 13:4954-4969. [PMID: 36187264 PMCID: PMC9484410 DOI: 10.1364/boe.462493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/08/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
The function of a biological cell is fundamentally defined by the structural architecture of packaged DNA in the nucleus. Elucidating information about the packaged DNA is facilitated by high-resolution imaging. Here, we combine and correlate hard X-ray propagation-based phase contrast tomography and visible light confocal microscopy in three dimensions to probe DNA in whole cell nuclei of NIH-3T3 fibroblasts. In this way, unlabeled and fluorescently labeled substructures within the cell are visualized in a complementary manner. Our approach enables the quantification of the electron density, volume and optical fluorescence intensity of nuclear material. By joining all of this information, we are able to spatially localize and physically characterize both active and inactive heterochromatin, euchromatin, pericentric heterochromatin foci and nucleoli.
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Affiliation(s)
- Andrew Wittmeier
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Marten Bernhardt
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Anna-Lena Robisch
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Chiara Cassini
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Germany
| | - Markus Osterhoff
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Tim Salditt
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Germany
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25
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Moraleva AA, Deryabin AS, Rubtsov YP, Rubtsova MP, Dontsova OA. Eukaryotic Ribosome Biogenesis: The 60S Subunit. Acta Naturae 2022; 14:39-49. [PMID: 35925480 PMCID: PMC9307984 DOI: 10.32607/actanaturae.11541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 02/11/2022] [Indexed: 11/20/2022] Open
Abstract
Ribosome biogenesis is consecutive coordinated maturation of ribosomal precursors in the nucleolus, nucleoplasm, and cytoplasm. The formation of mature ribosomal subunits involves hundreds of ribosomal biogenesis factors that ensure ribosomal RNA processing, tertiary structure, and interaction with ribosomal proteins. Although the main features and stages of ribosome biogenesis are conservative among different groups of eukaryotes, this process in human cells has become more complicated due to the larger size of the ribosomes and pre-ribosomes and intricate regulatory pathways affecting their assembly and function. Many of the factors involved in the biogenesis of human ribosomes have been identified using genome-wide screening based on RNA interference. A previous part of this review summarized recent data on the processing of the primary rRNA transcript and compared the maturation of the small 40S subunit in yeast and human cells. This part of the review focuses on the biogenesis of the large 60S subunit of eukaryotic ribosomes.
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Affiliation(s)
- A. A. Moraleva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Deryabin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - Yu. P. Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - M. P. Rubtsova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991 Russia
| | - O. A. Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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26
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Temaj G, Saha S, Dragusha S, Ejupi V, Buttari B, Profumo E, Beqa L, Saso L. Ribosomopathies and cancer: pharmacological implications. Expert Rev Clin Pharmacol 2022; 15:729-746. [PMID: 35787725 DOI: 10.1080/17512433.2022.2098110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The ribosome is a ribonucleoprotein organelle responsible for protein synthesis, and its biogenesis is a highly coordinated process that involves many macromolecular components. Any acquired or inherited impairment in ribosome biogenesis or ribosomopathies is associated with the development of different cancers and rare genetic diseases. Interference with multiple steps of protein synthesis has been shown to promote tumor cell death. AREAS COVERED We discuss the current insights about impaired ribosome biogenesis and their secondary consequences on protein synthesis, transcriptional and translational responses, proteotoxic stress, and other metabolic pathways associated with cancer and rare diseases. Studies investigating the modulation of different therapeutic chemical entities targeting cancer in in vitro and in vivo models have also been detailed. EXPERT OPINION Despite the association between inherited mutations affecting ribosome biogenesis and cancer biology, the development of therapeutics targeting the essential cellular machinery has only started to emerge. New chemical entities should be designed to modulate different checkpoints (translating oncoproteins, dysregulation of specific ribosome-assembly machinery, ribosomal stress, and rewiring ribosomal functions). Although safe and effective therapies are lacking, consideration should also be given to using existing drugs alone or in combination for long-term safety, with known risks for feasibility in clinical trials and synergistic effects.
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Affiliation(s)
| | - Sarmistha Saha
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | | | - Valon Ejupi
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Brigitta Buttari
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Elisabetta Profumo
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Lule Beqa
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University of Rome, Italy
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27
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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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Abstract
The nucleolus is best known for housing the highly ordered assembly line that produces ribosomal subunits. The >100 ribosome assembly factors in the nucleolus are thought to cycle between two states: an operative state (when integrated into subunit assembly intermediates) and a latent state (upon release from intermediates). Although it has become commonplace to refer to the nucleolus as "being a multilayered condensate," and this may be accurate for latent factors, there is little reason to think that such assertions pertain to the operative state of assembly factors.
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Affiliation(s)
- Alan Tartakoff
- Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Patrick DiMario
- Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Eduard Hurt
- Universität Heidelberg, Biochemistry Center, Heidelberg, Baden Württemberg 69120, Germany
| | - Brian McStay
- Centre for Chromosome Biology, Galway H91 TK33, Ireland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich CH-8057, Switzerland
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, United Kingdom
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29
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Transcriptomic analysis of ribosome biogenesis and pre-rRNA processing during growth stress in Entamoeba histolytica. Exp Parasitol 2022; 239:108308. [PMID: 35718007 DOI: 10.1016/j.exppara.2022.108308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 05/27/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022]
Abstract
Ribosome biogenesis, a multi-step process involving transcription, modification, folding and processing of rRNA, is the major consumer of cellular energy. It involves sequential assembly of ribosomal proteins (RP)s via more than 200 ribogenesis factors. Unlike model organisms where transcription of rRNA and RP genes slows down during stress, in Entamoeba histolytica, pre-rRNA synthesis continues, and unprocessed pre-rRNA accumulates. Northern hybridization from different spacer regions depicted the accumulation of unprocessed intermediates during stress. To gain insight into the vast repertoire of ribosome biogenesis factors and understand the major components playing role during stress we computationally identified ribosome biogenesis factors in E. histolytica. Of the ∼279 Saccharomyces cerevisiae proteins, we could only find 188 proteins in E. histolytica. Some of the proteins missing in E. histolytica were also missing in humans. A number of proteins represented by multiple genes in S. cerevisiae had a single copy in E. histolytica. Interestingly E. histolytica lacked mitochondrial ribosome biogenesis factors and had far less RNase components compared to S. cerevisiae. Transcriptomic studies revealed the differential regulation of ribosomal factors both in serum starved and RRP6 down-regulation conditions. These included the NEP1 and TSR3 proteins that chemically modify 18S-rRNA. Pre-rRNA precursors accumulate upon downregulation of the latter proteins in S. cerevisiae and humans. These data reveal the major factors that regulate pre-rRNA processing during stress in E. histolytica and provide the first complete repertoire of ribosome biogenesis factors in this early-branching protist.
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30
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Feric M, Misteli T. Function moves biomolecular condensates in phase space. Bioessays 2022; 44:e2200001. [PMID: 35243657 PMCID: PMC9277701 DOI: 10.1002/bies.202200001] [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: 01/03/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022]
Abstract
Phase separation underlies the formation of biomolecular condensates. We hypothesize the cellular processes that occur within condensates shape their structural features. We use the example of transcription to discuss structure-function relationships in condensates. Various types of transcriptional condensates have been reported across the evolutionary spectrum in the cell nucleus as well as in mitochondrial and bacterial nucleoids. In vitro and in vivo observations suggest that transcriptional activity of condensates influences their supramolecular structure, which in turn affects their function. Condensate organization thus becomes driven by differences in miscibility among the DNA and proteins of the transcription machinery and the RNA transcripts they generate. These considerations are in line with the notion that cellular processes shape the structural properties of condensates, leading to a dynamic, mutual interplay between structure and function in the cell.
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Affiliation(s)
- Marina Feric
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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31
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Subirana MA, Riemschneider S, Hause G, Dobritzsch D, Schaumlöffel D, Herzberg M. High spatial resolution imaging of subcellular macro and trace element distribution during phagocytosis. Metallomics 2022; 14:6530650. [PMID: 35179212 DOI: 10.1093/mtomcs/mfac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022]
Abstract
The bioavailability of trace elements in the course of evolution had an essential influence on the emergence of life itself. This is reflected in the co-evolution between eukaryotes and prokaryotes. In this study, the influence and cellular distribution of bioelements during phagocytosis at the host-pathogen interface was investigated using high-resolution nanoscale secondary ion mass spectrometry (NanoSIMS) and quantitative inductively coupled plasma mass spectrometry (ICP-MS). In the eukaryotic murine macrophages (RAW 264.7 cell line), the cellular Fe / Zn ratio was found to be balanced, whereas the dominance of iron in the prokaryotic cells of the pathogen Salmonella enterica Serovar Enteritidis was about 90% compared to zinc. This confirms the evolutionary increased zinc requirement of the eukaryotic animal cell. Using NanoSIMS, the Cs+ primary ion source allowed high spatial resolution mapping of cell morphology down to subcellular level. At a comparable resolution, several low abundant trace elements could be mapped during phagocytosis with a RF plasma O- primary ion source. An enrichment of copper and nickel could be detected in the prokaryotic cells. Surprisingly, an accumulation of cobalt in the area of nuclear envelope was observed indicating an interesting but still unknown distribution of this trace element in murine macrophages.
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Affiliation(s)
- Maria Angels Subirana
- CNRS, Université de Pau et des Pays de l'Adour, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), UMR 5254, 64000 Pau, France
| | - Sina Riemschneider
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), 04103 Leipzig, Germany
| | - Gerd Hause
- Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Dirk Dobritzsch
- Martin-Luther-University Halle-Wittenberg, Core Facility - Proteomic Mass Spectrometry, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Dirk Schaumlöffel
- CNRS, Université de Pau et des Pays de l'Adour, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), UMR 5254, 64000 Pau, France.,Peoples' Friendship University of Russia (RUDN University), Mklukho-Maklaya str. 6, 117198 Moscow, Russia
| | - Martin Herzberg
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Kurt-Mothes-Str. 3, 06120 Halle/Saale, Germany
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32
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Roqanian S, Ahmadian S, Nabavi SM, Pakdaman H, Shafiezadeh M, Goudarzi G, Shahpasand K. Tau nuclear translocation is a leading step in tau pathology process through P53 stabilization and nucleolar dispersion. J Neurosci Res 2022; 100:1084-1104. [PMID: 35170061 DOI: 10.1002/jnr.25024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022]
Abstract
Tau protein abnormalities are associated with various neurodegenerative disorders, including Alzheimer's disease (AD) and traumatic brain injury (TBI). In tau-overexpressing SHSY5Y cells and iPSC-derived neuron models of frontotemporal dementia (FTD), axonal tau translocates into the nuclear compartment, resulting in neuronal dysfunction. Despite extensive research, the mechanisms by which tau translocation results in neurodegeneration remain elusive thus far. We studied the nuclear displacement of different P-tau species [Cis phosphorylated Thr231-tau (cis P-tau), phosphorylated Ser202/Thr205-tau (AT8 P-tau), and phosphorylated Thr212/Ser214-tau (AT100 P-tau)] at various time points using starvation in primary cortical neurons and single severe TBI (ssTBI) in male mouse cerebral cortices as tauopathy models. While all P-tau species translocated into the somatodendritic compartment in response to stress, cis P-tau did so more rapidly than the other species. Notably, nuclear localization of P-tau was associated with p53 apoptotic stabilization and nucleolar stress, both of which resulted in neurodegeneration. In summary, our findings indicate that P-tau nuclear translocation results in p53-dependent apoptosis and nucleolar dispersion, which is consistent with neurodegeneration.
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Affiliation(s)
- Shaqayeq Roqanian
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.,Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Shahin Ahmadian
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Seyed Masood Nabavi
- Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hossein Pakdaman
- Brain Mapping Research Center, Department of Neurology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahshid Shafiezadeh
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ghazaleh Goudarzi
- Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Koorosh Shahpasand
- Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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33
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Brown IN, Lafita-Navarro MC, Conacci-Sorrell M. Regulation of Nucleolar Activity by MYC. Cells 2022; 11:cells11030574. [PMID: 35159381 PMCID: PMC8834138 DOI: 10.3390/cells11030574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 01/20/2023] Open
Abstract
The nucleolus harbors the machinery necessary to produce new ribosomes which are critical for protein synthesis. Nucleolar size, shape, and density are highly dynamic and can be adjusted to accommodate ribosome biogenesis according to the needs for protein synthesis. In cancer, cells undergo continuous proliferation; therefore, nucleolar activity is elevated due to their high demand for protein synthesis. The transcription factor and universal oncogene MYC promotes nucleolar activity by enhancing the transcription of ribosomal DNA (rDNA) and ribosomal proteins. This review summarizes the importance of nucleolar activity in mammalian cells, MYC’s role in nucleolar regulation in cancer, and discusses how a better understanding (and the potential inhibition) of aberrant nucleolar activity in cancer cells could lead to novel therapeutics.
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Affiliation(s)
- Isabella N. Brown
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - M. Carmen Lafita-Navarro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Correspondence: (M.C.L.-N.); (M.C.-S.)
| | - Maralice Conacci-Sorrell
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence: (M.C.L.-N.); (M.C.-S.)
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34
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Otellin VA, Khozhai LI, Shishko TT, Vershinina EA. Nucleolar Ultrastructure in Neurons of the Rat Neocortical Sensorimotor Area during the Neonatal Period after Perinatal Hypoxic Exposure and Its Pharmacological Correction. J EVOL BIOCHEM PHYS+ 2021. [DOI: 10.1134/s0022093021060053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Davidian AG, Dyomin AG, Galkina SA, Makarova NE, Dmitriev SE, Gaginskaya ER. 45S rDNA Repeats of Turtles and Crocodiles Harbor a Functional 5S rRNA Gene Specifically Expressed in Oocytes. Mol Biol Evol 2021; 39:6432055. [PMID: 34905062 PMCID: PMC8789306 DOI: 10.1093/molbev/msab324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In most eukaryotic genomes, tandemly repeated copies of 5S rRNA genes are clustered outside the nucleolus organizer region (NOR), which normally encodes three other major rRNAs: 18S, 5.8S, and 28S. Our analysis of turtle rDNA sequences has revealed a 5S rDNA insertion into the NOR intergenic spacer in antisense orientation. The insertion (hereafter called NOR-5S rRNA gene) has a length of 119 bp and coexists with the canonical 5S rDNA clusters outside the NOR. Despite the ∼20% nucleotide difference between the two 5S gene sequences, their internal control regions for RNA polymerase III are similar. Using the turtle Trachemys scripta as a model species, we showed the NOR-5S rDNA specific expression in oocytes. This expression is concurrent with the NOR rDNA amplification during oocyte growth. We show that in vitellogenic oocytes, the NOR-5S rRNA prevails over the canonical 5S rRNA in the ribosomes, suggesting a role of modified ribosomes in oocyte-specific translation. The orders Testudines and Crocodilia seem to be the only taxa of vertebrates with such a peculiar rDNA organization. We speculate that the amplification of the 5S rRNA genes as a part of the NOR DNA during oogenesis provides a dosage balance between transcription of all the four ribosomal RNAs while producing a maternal pool of extra ribosomes. We further hypothesize that the NOR-5S rDNA insertion appeared in the Archelosauria clade during the Permian period and was lost later in the ancestors of Aves.
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Affiliation(s)
- Asya G Davidian
- Biological Faculty, Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexander G Dyomin
- Laboratory of Cell Technologies, Saratov State Medical University, Saratov, Russia
| | - Svetlana A Galkina
- Biological Faculty, Saint Petersburg State University, Saint Petersburg, Russia
| | - Nadezhda E Makarova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Elena R Gaginskaya
- Biological Faculty, Saint Petersburg State University, Saint Petersburg, Russia
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36
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Chen L, Li Z, Zeng T, Zhang YH, Zhang S, Huang T, Cai YD. Predicting Human Protein Subcellular Locations by Using a Combination of Network and Function Features. Front Genet 2021; 12:783128. [PMID: 34804131 PMCID: PMC8603309 DOI: 10.3389/fgene.2021.783128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Given the limitation of technologies, the subcellular localizations of proteins are difficult to identify. Predicting the subcellular localization and the intercellular distribution patterns of proteins in accordance with their specific biological roles, including validated functions, relationships with other proteins, and even their specific sequence characteristics, is necessary. The computational prediction of protein subcellular localizations can be performed on the basis of the sequence and the functional characteristics. In this study, the protein-protein interaction network, functional annotation of proteins and a group of direct proteins with known subcellular localization were used to construct models. To build efficient models, several powerful machine learning algorithms, including two feature selection methods, four classification algorithms, were employed. Some key proteins and functional terms were discovered, which may provide important contributions for determining protein subcellular locations. Furthermore, some quantitative rules were established to identify the potential subcellular localizations of proteins. As the first prediction model that uses direct protein annotation information (i.e., functional features) and STRING-based protein-protein interaction network (i.e., network features), our computational model can help promote the development of predictive technologies on subcellular localizations and provide a new approach for exploring the protein subcellular localization patterns and their potential biological importance.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai, China
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - ZhanDong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Tao Zeng
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - ShiQi Zhang
- Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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37
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Suganuma T, Swanson SK, Gogol M, Garrett TJ, Florens L, Workman JL. MOCS2 links nucleotide metabolism to nucleoli function. J Mol Cell Biol 2021; 13:838-840. [PMID: 34698840 DOI: 10.1093/jmcb/mjab069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/27/2021] [Accepted: 09/14/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tamaki Suganuma
- Stowers Institute for Medical Research, Kansas City, MO, 64110 USA
| | - Selene K Swanson
- Stowers Institute for Medical Research, Kansas City, MO, 64110 USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, Kansas City, MO, 64110 USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, 32610 USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO, 64110 USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO, 64110 USA
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38
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Chen L, Jin C, Liu H, Feng R, Li Z, Zhang J. Analysis of the role of Ly-1 antibody reactive in different cancer types. Bioengineered 2021; 12:9452-9462. [PMID: 34696677 PMCID: PMC8809990 DOI: 10.1080/21655979.2021.1995100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
LYAR (Ly-1 antibody reactive) is a transcription factor with a specific DNA-binding domain, which plays a key role in the regulation of embryonic stem cell self-renewal and differentiation. However, the role of LYAR in human cancers remains unclear. This study aimed to analyze the prognostic value of LYAR in cancer. In this study, we evaluated the prognostic value of LYAR in various tumors. We research found that, compared with normal tissues, LYAR levels werehigher in a variety of tumors. LYAR expression level was associated with poor overall survival, progression-free interval, and disease-specific survival. LYAR expression was also related to tumor grade, stage, age, and tumor status. Cell counting kit-8, Transwell, and wound healing assay showed that knocking out LYAR significantly inhibited the proliferation, migration, and invasion of hepatocellular carcinoma cells. In addition, this study found that LYARexpression was significantly positively correlated with MKI67IP, BZW2, and CCT2. Gene set enrichment analysis results showed that samples with high LYAR expression levels were rich in spliceosomes, RNA degradation, pyrimidine metabolism, cell cycle, nucleotide excision repair, and base excision repair.
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Affiliation(s)
- Linlin Chen
- General Surgery, Affiliated Hospital of West Anhui Health Vocational College, Luan,237000, China.,West Anhui Health Vocational College, Luan, 237000, China
| | - Congwen Jin
- General Surgery, Affiliated Hospital of West Anhui Health Vocational College, Luan,237000, China.,West Anhui Health Vocational College, Luan, 237000, China
| | - Hao Liu
- General Surgery, Affiliated Hospital of West Anhui Health Vocational College, Luan,237000, China.,West Anhui Health Vocational College, Luan, 237000, China
| | - Rongmei Feng
- Critical Care Medicine, The Lu'an Hospital Affiliated to Anhui Medical University, Luan,237000, China.,Critical Care Medicine, The Lu'an People's Hospital, Luan,237000, China
| | - Zhengdong Li
- General Surgery, Affiliated Hospital of West Anhui Health Vocational College, Luan,237000, China.,West Anhui Health Vocational College, Luan, 237000, China
| | - Jiasheng Zhang
- Emergency surgery, The Lu'an Hospital Affiliated to Anhui Medical University, Luan,237000, China.,Emergency surgery, The Lu'an People's Hospital, Luan,237000, China
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39
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Floro J, Dai A, Metzger A, Mora-Martin A, Ganem N, Cifuentes D, Wu CS, Dalal J, Lyons S, Labadorf A, Flynn R. SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing. Nucleic Acids Res 2021; 49:9424-9443. [PMID: 34365507 PMCID: PMC8450105 DOI: 10.1093/nar/gkab647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 07/08/2021] [Accepted: 07/21/2021] [Indexed: 11/22/2022] Open
Abstract
RNA provides the framework for the assembly of some of the most intricate macromolecular complexes within the cell, including the spliceosome and the mature ribosome. The assembly of these complexes relies on the coordinated association of RNA with hundreds of trans-acting protein factors. While some of these trans-acting factors are RNA-binding proteins (RBPs), others are adaptor proteins, and others still, function as both. Defects in the assembly of these complexes results in a number of human pathologies including neurodegeneration and cancer. Here, we demonstrate that Silencing Defective 2 (SDE2) is both an RNA binding protein and also a trans-acting adaptor protein that functions to regulate RNA splicing and ribosome biogenesis. SDE2 depletion leads to widespread changes in alternative splicing, defects in ribosome biogenesis and ultimately complete loss of cell viability. Our data highlight SDE2 as a previously uncharacterized essential gene required for the assembly and maturation of the complexes that carry out two of the most fundamental processes in mammalian cells.
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Affiliation(s)
- Jess Floro
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anqi Dai
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
- Bioinformatics Program, Boston University, Boston, MA 02118 USA
| | - Abigail Metzger
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Alexandra Mora-Martin
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Neil J Ganem
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ching-Shyi Wu
- Department and Graduate Institute of Pharmacology, National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Jasbir Dalal
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Shawn M Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Adam Labadorf
- Bioinformatics Program, Boston University, Boston, MA 02118 USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118 USA
| | - Rachel L Flynn
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
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40
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Nieto B, Gaspar SG, Sapio RT, Clavaín L, Bustelo XR, Pestov DG, Dosil M. Efficient fractionation and analysis of ribosome assembly intermediates in human cells. RNA Biol 2021; 18:182-197. [PMID: 34530680 PMCID: PMC8682975 DOI: 10.1080/15476286.2021.1965754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Biochemical studies of the human ribosome synthesis pathway have been hindered by technical difficulties in obtaining intact preribosomal complexes from internal regions of the nucleolus. Here we provide a detailed description of an extraction method that enables efficient detection, isolation, and characterization of nucleolar preribosomes containing large pre-rRNA species. The three-step Preribosome Sequential Extraction (PSE) protocol preserves the integrity of early preribosomal complexes and yields preparations amenable to biochemical analyses from low amounts of starting material. We validate this procedure through the detection of specific trans-acting factors and pre-rRNAs in the extracted preribosomes using affinity matrix pull-downs and sedimentation assays. In addition, we describe the application of the PSE method for monitoring cellular levels of ribosome-free 5S RNP complexes as an indicator of ribosome biogenesis stress. Our optimized experimental procedures will facilitate studies of human ribosome biogenesis in normal, mutant and stressed-cell scenarios, including the characterization of candidate ribosome biogenesis factors, preribosome interactors under specific physiological conditions or effects of drugs on ribosome maturation.
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Affiliation(s)
- Blanca Nieto
- Centro de Investigación del Cáncer, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain
| | - Sonia G Gaspar
- Centro de Investigación del Cáncer, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain
| | - Russell T Sapio
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, USA.,Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, USA
| | - Laura Clavaín
- Centro de Investigación del Cáncer, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Centro de Investigación del Cáncer, Salamanca, Spain
| | - Xosé R Bustelo
- Centro de Investigación del Cáncer, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Centro de Investigación del Cáncer, Salamanca, Spain
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, USA
| | - Mercedes Dosil
- Centro de Investigación del Cáncer, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Centro de Investigación del Cáncer, Salamanca, Spain.,Departamento de Bioquímica y Biología Molecular, University of Salamanca, Salamanca, Spain
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41
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Faria JRC. A nuclear enterprise: zooming in on nuclear organization and gene expression control in the African trypanosome. Parasitology 2021; 148:1237-1253. [PMID: 33407981 PMCID: PMC8311968 DOI: 10.1017/s0031182020002437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 12/17/2022]
Abstract
African trypanosomes are early divergent protozoan parasites responsible for high mortality and morbidity as well as a great economic burden among the world's poorest populations. Trypanosomes undergo antigenic variation in their mammalian hosts, a highly sophisticated immune evasion mechanism. Their nuclear organization and mechanisms for gene expression control present several conventional features but also a number of striking differences to the mammalian counterparts. Some of these unorthodox characteristics, such as lack of controlled transcription initiation or enhancer sequences, render their monogenic antigen transcription, which is critical for successful antigenic variation, even more enigmatic. Recent technological developments have advanced our understanding of nuclear organization and gene expression control in trypanosomes, opening novel research avenues. This review is focused on Trypanosoma brucei nuclear organization and how it impacts gene expression, with an emphasis on antigen expression. It highlights several dedicated sub-nuclear bodies that compartmentalize specific functions, whilst outlining similarities and differences to more complex eukaryotes. Notably, understanding the mechanisms underpinning antigen as well as general gene expression control is of great importance, as it might help designing effective control strategies against these organisms.
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Affiliation(s)
- Joana R. C. Faria
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, DundeeDD1 5EH, UK
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42
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Wang R, Huang A, Wang Y, Mei P, Zhu H, Chen Q, Xu S. High-Resolution Microscopy to Learn the Nuclear Organization of the Living Yeast Cells. Stem Cells Int 2021; 2021:9951114. [PMID: 34497652 PMCID: PMC8421178 DOI: 10.1155/2021/9951114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/07/2021] [Indexed: 11/18/2022] Open
Abstract
The spatial organization of the nucleus is a key determinant in all genome activities. However, the accurate measurement of the nuclear organization is still technically challenging. Here, the technology NucQuant we created previously was utilized to detect the variation of the nuclear organization, including the heterogeneity of the nuclear geometry, the change of the NPC distribution along different cell cycle stages during interphase, and the organization of the nucleolus. The results confirmed that not only the growth rate and the NPC distribution are influenced by the carbon source; the nuclear shape is also impacted by the carbon source. The nuclei lost their spherical geometry gradually when the cell was cultured from the most to a less favorable carbon source. We also discovered that the nucleolus prefers to locate at the nuclear periphery, which was called the "genes poor region," especially when the cells entered quiescence. Furthermore, the distribution of the NPC along the different stages during the interphase was analyzed. We proposed that with the growth of the cell, the nucleus would grow from the surface of the NE flanking the nucleolus firstly.
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Affiliation(s)
- Renjie Wang
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - Aiwen Huang
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - Yan Wang
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - Pengxin Mei
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - He Zhu
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - Qianqian Chen
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
| | - Sankui Xu
- College of Materials Science & Engineering, Henan University of Technology, Zhengzhou, China
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43
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Jin M, Li J, Chen Y, Zhao J, Zhang J, Zhang Z, Du P, Zhang L, Lu X. Near-Infrared Small Molecule as a Specific Fluorescent Probe for Ultrasensitive Recognition of Antiparallel Human Telomere G-Quadruplexes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:32743-32752. [PMID: 34228441 DOI: 10.1021/acsami.1c07101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In the past 10 years, many fluorescent probes have been developed to recognize G-quadruplexes (G4s) since G4s play an important role in biological systems. However, the selectivity and sensitivity of existing probes for G4s limit their further applications. Herein, we design and synthesize a new probe (TOVJ) by introducing 9-vinyljulolidine into TO. The new probe exhibits almost no fluorescence in an aqueous solution. Upon interacting with G4s, especially the antiparallel G4s, the fluorescence intensity was greatly enhanced (maximum 2742-fold) with a large Stokes shift of 198 nm and the maximum emission peak at 694 nm (near-infrared region). TOVJ showed high sensitivity and selectivity to G4s over other DNA topologies (ssDNA/dsDNA), especially to antiparallel G4s. For antiparallel human telomere G4 detection, the limits of detection of Hum24 and 22AG Na+ were as low as 164 and 231 pM, respectively. This indicates that TOVJ is a highly sensitive fluorescence sensor that can be effectively used for antiparallel human telomere G4 detection. The result of live-cell imaging showed that TOVJ could enter live cells and locate in the mitochondria.
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Affiliation(s)
- Ming Jin
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jing Li
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Yang Chen
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jie Zhao
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jiahui Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Zhen Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Peiyao Du
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Libing Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Xiaoquan Lu
- Key Laboratory of Bioelectrochemistry and Environmental Analysis of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, People's Republic of China
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44
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He H, Chen X, Feng Z, Liu L, Wang Q, Bi S. Nanoscopic Imaging of Nucleolar Stress Enabled by Protein-Mimicking Carbon Dots. NANO LETTERS 2021; 21:5689-5696. [PMID: 34181434 DOI: 10.1021/acs.nanolett.1c01420] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The nucleolus is a central hub for coordinating cellular stress responses during cancer development and treatment. Accurate identification of nucleolar stress response is crucially desired for nucleolus-based diagnostics and therapeutics but technically challenging due to the need to address the ultrastructural analysis. Here, we report a protein-like CD with the integration of fluorescent blinking domains and RNA-binding motifs, which offers the ability to perform enhanced super-resolution imaging of the nucleolar ultrastructure. This image allows extraction of multidimensional information from the nucleolus for accurate distinguishment of different cells from the same cell types. Furthermore, we demonstrate for the first time this CD-depicted nucleolar ultrastructure as a sensitive hallmark to identify and discriminate subtle responses to various stressors as well as to afford RNA-related information that has been inaccessible by conventional immunofluorescence methods. This protein-mimicking CD could become a broadly useful probe for nucleolar stress studies in cell diagnostics and therapeutics.
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Affiliation(s)
- Hua He
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaoliang Chen
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Zhenzhen Feng
- Technical Center of Qingdao Customs District, Qingdao 266500, China
| | - Lihua Liu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Qian Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Simin Bi
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
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45
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Tartakoff AM, Chen L, Raghavachari S, Gitiforooz D, Dhinakaran A, Ni CL, Pasadyn C, Mahabeleshwar GH, Pasadyn V, Woolford JL. The nucleolus as a polarized coaxial cable in which the rDNA axis is surrounded by dynamic subunit-specific phases. Curr Biol 2021; 31:2507-2519.e4. [PMID: 33862007 PMCID: PMC8222187 DOI: 10.1016/j.cub.2021.03.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/18/2021] [Accepted: 03/11/2021] [Indexed: 12/24/2022]
Abstract
In ribosomal DNA (rDNA) repeats, sequences encoding small-subunit (SSU) rRNA precede those encoding large-subunit (LSU) rRNAs. Processing the composite transcript and subunit assembly requires >100 subunit-specific nucleolar assembly factors (AFs). To investigate the functional organization of the nucleolus, we localized AFs in S. cerevisiae in which the rDNA axis was "linearized" to reduce its dimensionality, thereby revealing its coaxial organization. In this situation, rRNA synthesis and processing continue. The axis is embedded in an inner layer/phase of SSU AFs that is surrounded by an outer layer/phase of LSU AFs. When subunit production is inhibited, subsets of AFs differentially relocate between the inner and outer layers, as expected if there is a cycle of repeated relocation whereby "latent" AFs become "operative" when recruited to nascent subunits. Recognition of AF cycling and localization of segments of rRNA make it possible to infer the existence of assembly intermediates that span between the inner and outer layers and to chart the cotranscriptional assembly of each subunit. AF cycling also can explain how having more than one protein phase in the nucleolus makes possible "vectorial 2-phase partitioning" as a driving force for relocation of nascent rRNPs. Because nucleoplasmic AFs are also present in the outer layer, we propose that critical surface remodeling occurs at this site, thereby partitioning subunit precursors into the nucleoplasm for post-transcriptional maturation. Comparison to observations on higher eukaryotes shows that the coaxial paradigm is likely to be applicable for the many other organisms that have rDNA repeats.
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Affiliation(s)
- Alan M Tartakoff
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA.
| | - Lan Chen
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Shashank Raghavachari
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Daria Gitiforooz
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Akshyasri Dhinakaran
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Chun-Lun Ni
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | | | - Ganapati H Mahabeleshwar
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Vanessa Pasadyn
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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Ali MAM, Garcia-Vilas JA, Cromwell CR, Hubbard BP, Hendzel MJ, Schulz R. Matrix metalloproteinase-2 mediates ribosomal RNA transcription by cleaving nucleolar histones. FEBS J 2021; 288:6736-6751. [PMID: 34101354 DOI: 10.1111/febs.16061] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/09/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Cell proliferation and survival require continuous ribosome biogenesis and protein synthesis. Genes encoding ribosomal RNA are physically located in a specialized substructure within the nucleus known as the nucleolus, which has a central role in the biogenesis of ribosomes. Matrix metalloproteinase-2 was previously detected in the nucleus, however, its role there is elusive. Herein we report that matrix metalloproteinase-2 resides within the nucleolus to regulate ribosomal RNA transcription. Matrix metalloproteinase-2 is enriched at the promoter region of ribosomal RNA gene repeats, and its inhibition downregulates preribosomal RNA transcription. The N-terminal tail of histone H3 is clipped by matrix metalloproteinase-2 in the nucleolus, which is associated with increased ribosomal RNA transcription. Knocking down/out matrix metalloproteinase-2, or inhibiting its activity, prevents histone H3 cleavage and reduces both ribosomal RNA transcription and cell proliferation. In addition to the known extracellular roles of matrix metalloproteinase-2 in tumor growth, our data reveal an epigenetic mechanism whereby intranucleolar matrix metalloproteinase-2 regulates cell proliferation through histone clipping and facilitation of ribosomal RNA transcription.
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Affiliation(s)
- Mohammad A M Ali
- Department of Pediatrics, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada.,Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York, Binghamton, NY, USA
| | - Javier A Garcia-Vilas
- Department of Pediatrics, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada.,Department of Pharmacology, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Christopher R Cromwell
- Department of Pharmacology, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Basil P Hubbard
- Department of Pharmacology, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Michael J Hendzel
- Department of Oncology, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Richard Schulz
- Department of Pediatrics, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada.,Department of Pharmacology, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
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Kemp JP, Yang XC, Dominski Z, Marzluff WF, Duronio RJ. Superresolution light microscopy of the Drosophila histone locus body reveals a core-shell organization associated with expression of replication-dependent histone genes. Mol Biol Cell 2021; 32:942-955. [PMID: 33788585 PMCID: PMC8108526 DOI: 10.1091/mbc.e20-10-0645] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The histone locus body (HLB) is an evolutionarily conserved nuclear body that regulates the transcription and processing of replication-dependent (RD) histone mRNAs, which are the only eukaryotic mRNAs lacking a poly-A tail. Many nuclear bodies contain distinct domains, but how internal organization is related to nuclear body function is not fully understood. Here, we demonstrate using structured illumination microscopy that Drosophila HLBs have a “core–shell” organization in which the internal core contains transcriptionally active RD histone genes. The N-terminus of Mxc, which contains a domain required for Mxc oligomerization, HLB assembly, and RD histone gene expression, is enriched in the HLB core. In contrast, the C-terminus of Mxc is enriched in the HLB outer shell as is FLASH, a component of the active U7 snRNP that cotranscriptionally cleaves RD histone pre-mRNA. Consistent with these results, we show biochemically that FLASH binds directly to the Mxc C-terminal region. In the rapid S-M nuclear cycles of syncytial blastoderm Drosophila embryos, the HLB disassembles at mitosis and reassembles the core–shell arrangement as histone gene transcription is activated immediately after mitosis. Thus, the core–shell organization is coupled to zygotic histone gene transcription, revealing a link between HLB internal organization and RD histone gene expression.
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Affiliation(s)
- James P Kemp
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Zbigniew Dominski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Robert J Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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48
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Kim ES, Chung CG, Park JH, Ko BS, Park SS, Kim YH, Cha IJ, Kim J, Ha CM, Kim HJ, Lee SB. C9orf72-associated arginine-rich dipeptide repeats induce RNA-dependent nuclear accumulation of Staufen in neurons. Hum Mol Genet 2021; 30:1084-1100. [PMID: 33783499 PMCID: PMC8188407 DOI: 10.1093/hmg/ddab089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/24/2022] Open
Abstract
RNA-binding proteins (RBPs) play essential roles in diverse cellular processes through post-transcriptional regulation of RNAs. The subcellular localization of RBPs is thus under tight control, the breakdown of which is associated with aberrant cytoplasmic accumulation of nuclear RBPs such as TDP-43 and FUS, well-known pathological markers for amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). Here, we report in Drosophila model for ALS/FTD that nuclear accumulation of a cytoplasmic RBP Staufen may be a new pathological feature. We found that in Drosophila C4da neurons expressing PR36, one of the arginine-rich dipeptide repeat proteins (DPRs), Staufen accumulated in the nucleus in Importin- and RNA-dependent manner. Notably, expressing Staufen with exogenous NLS—but not with mutated endogenous NLS—potentiated PR-induced dendritic defect, suggesting that nuclear-accumulated Staufen can enhance PR toxicity. PR36 expression increased Fibrillarin staining in the nucleolus, which was enhanced by heterozygous mutation of stau (stau+/−), a gene that codes Staufen. Furthermore, knockdown of fib, which codes Fibrillarin, exacerbated retinal degeneration mediated by PR toxicity, suggesting that increased amount of Fibrillarin by stau+/− is protective. stau+/− also reduced the amount of PR-induced nuclear-accumulated Staufen and mitigated retinal degeneration and rescued viability of flies expressing PR36. Taken together, our data show that nuclear accumulation of Staufen in neurons may be an important pathological feature contributing to the pathogenesis of ALS/FTD.
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Affiliation(s)
- Eun Seon Kim
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea.,Dementia research group, Korea Brain Research Institute (KBRI), Daegu 41068, Republic of Korea
| | - Chang Geon Chung
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Jeong Hyang Park
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Byung Su Ko
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Sung Soon Park
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Yoon Ha Kim
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - In Jun Cha
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Jaekwang Kim
- Dementia research group, Korea Brain Research Institute (KBRI), Daegu 41068, Republic of Korea
| | - Chang Man Ha
- Research Division and Brain Research Core Facilities of Korea Brain Research Institute (KBRI), Daegu 41068, Republic of Korea
| | - Hyung-Jun Kim
- Dementia research group, Korea Brain Research Institute (KBRI), Daegu 41068, Republic of Korea
| | - Sung Bae Lee
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea.,Dementia research group, Korea Brain Research Institute (KBRI), Daegu 41068, Republic of Korea
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49
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FoxA2 and RNA Pol II mediate human islet amyloid polypeptide turnover in ER-stressed pancreatic β-cells. Biochem J 2021; 478:1261-1282. [PMID: 33650632 DOI: 10.1042/bcj20200984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 12/25/2022]
Abstract
Here, we investigated transcriptional and trafficking mechanisms of human islet amyloid polypeptide (hIAPP) in normal and stressed β-cells. In high glucose-challenged human islets and rat insulinoma cells overexpressing hIAPP, cell fractionation studies revealed increased accumulation of hIAPP. Unexpectedly, a significant fraction (up to 22%) of hIAPP was found in the nuclear soluble and chromatin-enriched fractions of cultured human islet and rat insulinoma cells. The nucleolar accumulation of monomeric forms of hIAPP did not have any adverse effect on the proliferation of β-cells nor did it affect nucleolar organization or function. However, intact nucleolar organization and function were essential for hIAPP expression under normal and ER-stress conditions as RNA polymerase II inhibitor, α-amanitin, reduced hIAPP protein expression evoked by high glucose and thapsigargin. Promoter activity studies revealed the essential role of transcription factor FoxA2 in hIAPP promoter activation in ER-stressed β-cells. Transcriptome and secretory studies demonstrate that the biosynthetic and secretory capacity of islet β-cells was preserved during ER stress. Thus, the main reason for increased intracellular hIAPP accumulation is its enhanced biosynthesis under these adverse conditions.
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Wittmeier A, Cassini C, Töpperwien M, Denz M, Hagemann J, Osterhoff M, Salditt T, Köster S. Combined scanning small-angle X-ray scattering and holography probes multiple length scales in cell nuclei. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:518-529. [PMID: 33650565 PMCID: PMC7941289 DOI: 10.1107/s1600577520016276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
X-rays are emerging as a complementary probe to visible-light photons and electrons for imaging biological cells. By exploiting their small wavelength and high penetration depth, it is possible to image whole, intact cells and resolve subcellular structures at nanometer resolution. A variety of X-ray methods for cell imaging have been devised for probing different properties of biological matter, opening up various opportunities for fully exploiting different views of the same sample. Here, a combined approach is employed to study cell nuclei of NIH-3T3 fibroblasts. Scanning small-angle X-ray scattering is combined with X-ray holography to quantify length scales, aggregation state, and projected electron and mass densities of the nuclear material. Only by joining all this information is it possible to spatially localize nucleoli, heterochromatin and euchromatin, and physically characterize them. It is thus shown that for complex biological systems, like the cell nucleus, combined imaging approaches are highly valuable.
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Affiliation(s)
- Andrew Wittmeier
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Chiara Cassini
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence ‘Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC)’, University of Göttingen, Göttingen, Germany
| | - Mareike Töpperwien
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Manuela Denz
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Johannes Hagemann
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Markus Osterhoff
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Tim Salditt
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence ‘Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC)’, University of Göttingen, Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence ‘Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC)’, University of Göttingen, Göttingen, Germany
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