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Lessenger AT, Swaffer MP, Skotheim JM, Feldman JL. Somatic polyploidy supports biosynthesis and tissue function by increasing transcriptional output. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586714. [PMID: 38585999 PMCID: PMC10996643 DOI: 10.1101/2024.03.25.586714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cell size and biosynthetic capacity generally increase with increased DNA content. Polyploidy has therefore been proposed to be an adaptive strategy to increase cell size in specialized tissues with high biosynthetic demands. However, if and how DNA concentration limits cellular biosynthesis in vivo is not well understood, and the impacts of polyploidy in non-disease states is not well studied. Here, we show that polyploidy in the C. elegans intestine is critical for cell growth and yolk biosynthesis, a central role of this organ. Artificially lowering the DNA/cytoplasm ratio by reducing polyploidization in the intestine gave rise to smaller cells with more dilute mRNA. Highly-expressed transcripts were more sensitive to this mRNA dilution, whereas lowly-expressed genes were partially compensated - in part by loading more RNA Polymerase II on the remaining genomes. DNA-dilute cells had normal total protein concentration, which we propose is achieved by increasing production of translational machinery at the expense of specialized, cell-type specific proteins.
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2
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Rahman MM, Balachandran RS, Stevenson JB, Kim Y, Proenca RB, Hedgecock EM, Kipreos ET. The Caenorhabditis elegans cullin-RING ubiquitin ligase CRL4DCAF-1 is required for proper germline nucleolus morphology and male development. Genetics 2023; 225:iyad126. [PMID: 37433110 PMCID: PMC10686702 DOI: 10.1093/genetics/iyad126] [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: 06/08/2023] [Revised: 06/08/2023] [Accepted: 07/02/2023] [Indexed: 07/13/2023] Open
Abstract
Cullin-RING ubiquitin ligases (CRLs) are the largest class of ubiquitin ligases with diverse functions encompassing hundreds of cellular processes. Inactivation of core components of the CRL4 ubiquitin ligase produces a germ cell defect in Caenorhabditis elegans that is marked by abnormal globular morphology of the nucleolus and fewer germ cells. We identified DDB1 Cullin4 associated factor (DCAF)-1 as the CRL4 substrate receptor that ensures proper germ cell nucleolus morphology. We demonstrate that the dcaf-1 gene is the ncl-2 (abnormal nucleoli) gene, whose molecular identity was not previously known. We also observed that CRL4DCAF-1 is required for male tail development. Additionally, the inactivation of CRL4DCAF-1 results in a male-specific lethality in which a percentage of male progeny arrest as embryos or larvae. Analysis of the germ cell nucleolus defect using transmission electron microscopy revealed that dcaf-1 mutant germ cells possess significantly fewer ribosomes, suggesting a defect in ribosome biogenesis. We discovered that inactivation of the sperm-fate specification gene fog-1 (feminization of the germ line-1) or its protein-interacting partner, fog-3, rescues the dcaf-1 nucleolus morphology defect. Epitope-tagged versions of both FOG-1 and FOG-3 proteins are aberrantly present in adult dcaf-1(RNAi) animals, suggesting that DCAF-1 negatively regulates FOG-1 and FOG-3 expression. Murine CRL4DCAF-1 targets the degradation of the ribosome assembly factor periodic trptophan protein 1 (PWP1). We observed that the inactivation of Caenorhabditis elegansDCAF-1 increases the nucleolar levels of PWP1 in the germ line, intestine, and hypodermis. Reducing the level of PWP-1 rescues the dcaf-1 mutant defects of fewer germ cell numbers and abnormal nucleolus morphology, suggesting that the increase in PWP-1 levels contributes to the dcaf-1 germline defect. Our results suggest that CRL4DCAF-1 has an evolutionarily ancient role in regulating ribosome biogenesis including a conserved target in PWP1.
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Affiliation(s)
- Mohammad M Rahman
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Riju S Balachandran
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | | | - Youngjo Kim
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Rui B Proenca
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Edward M Hedgecock
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Edward T Kipreos
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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3
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Xu D, Chen X, Kuang Y, Hong M, Xu T, Wang K, Huang X, Fu C, Ruan K, Zhu C, Feng X, Guang S. rRNA intermediates coordinate the formation of nucleolar vacuoles in C. elegans. Cell Rep 2023; 42:112915. [PMID: 37537842 DOI: 10.1016/j.celrep.2023.112915] [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: 04/17/2023] [Revised: 07/03/2023] [Accepted: 07/17/2023] [Indexed: 08/05/2023] Open
Abstract
The nucleolus is the most prominent membraneless organelle within the nucleus. How the nucleolar structure is regulated is poorly understood. Here, we identified two types of nucleoli in C. elegans. Type I nucleoli are spherical and do not have visible nucleolar vacuoles (NoVs), and rRNA transcription and processing factors are evenly distributed throughout the nucleolus. Type II nucleoli contain vacuoles, and rRNA transcription and processing factors exclusively accumulate in the periphery rim. The NoV contains nucleoplasmic proteins and is capable of exchanging contents with the nucleoplasm. The high-order structure of the nucleolus is dynamically regulated in C. elegans. Faithful rRNA processing is important to prohibit NoVs. The depletion of 27SA2 rRNA processing factors resulted in NoV formation. The inhibition of RNA polymerase I (RNAPI) transcription and depletion of two conserved nucleolar factors, nucleolin and fibrillarin, prohibits the formation of NoVs. This finding provides a mechanism to coordinate structure maintenance and gene expression.
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Affiliation(s)
- Demin Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xiangyang Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yan Kuang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Minjie Hong
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ting Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ke Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xinya Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chuanhai Fu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ke Ruan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chengming Zhu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Xuezhu Feng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Shouhong Guang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Hefei, Anhui 230027, China.
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4
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Vertti-Quintero N, Berger S, Casadevall I Solvas X, Statzer C, Annis J, Ruppen P, Stavrakis S, Ewald CY, Gunawan R, deMello AJ. Stochastic and Age-Dependent Proteostasis Decline Underlies Heterogeneity in Heat-Shock Response Dynamics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102145. [PMID: 34196492 DOI: 10.1002/smll.202102145] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Significant non-genetic stochastic factors affect aging, causing lifespan differences among individuals, even those sharing the same genetic and environmental background. In Caenorhabditis elegans, differences in heat-shock response (HSR) are predictive of lifespan. However, factors contributing to the heterogeneity of HSR are still not fully elucidated. Here, the authors characterized HSR dynamics in isogenic C. elegans expressing GFP reporter for hsp-16.2 for identifying the key contributors of HSR heterogeneity. Specifically, microfluidic devices that enable cross-sectional and longitudinal measurements of HSR dynamics in C. elegans at different scales are developed: in populations, within individuals, and in embryos. The authors adapted a mathematical model of HSR to single C. elegans and identified model parameters associated with proteostasis-maintenance of protein homeostasis-more specifically, protein turnover, as the major drivers of heterogeneity in HSR dynamics. It is verified that individuals with enhanced proteostasis fidelity in early adulthood live longer. The model-based comparative analysis of protein turnover in day-1 and day-2 adult C. elegans revealed a stochastic-onset of age-related proteostasis decline that increases the heterogeneity of HSR capacity. Finally, the analysis of C. elegans embryos showed higher HSR and proteostasis capacity than young adults and established transgenerational contribution to HSR heterogeneity that depends on maternal age.
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Affiliation(s)
| | - Simon Berger
- Institute of Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Xavier Casadevall I Solvas
- Institute of Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
- Department of Biosystems, KU Leuven, Leuven, B-3001, Belgium
| | - Cyril Statzer
- Institute of Translational Medicine, ETH Zurich, Schwerzenbach, 8603, Switzerland
| | - Jillian Annis
- Department of Chemical and Biological Engineering, University at Buffalo - SUNY, Buffalo, NY, 14260, USA
| | - Peter Ruppen
- Institute of Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Stavros Stavrakis
- Institute of Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Collin Y Ewald
- Institute of Translational Medicine, ETH Zurich, Schwerzenbach, 8603, Switzerland
| | - Rudiyanto Gunawan
- Institute of Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
- Department of Chemical and Biological Engineering, University at Buffalo - SUNY, Buffalo, NY, 14260, USA
| | - Andrew J deMello
- Institute of Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
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5
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Puente-Bedia A, Berciano MT, Tapia O, Martínez-Cué C, Lafarga M, Rueda N. Nuclear Reorganization in Hippocampal Granule Cell Neurons from a Mouse Model of Down Syndrome: Changes in Chromatin Configuration, Nucleoli and Cajal Bodies. Int J Mol Sci 2021; 22:ijms22031259. [PMID: 33514010 PMCID: PMC7865916 DOI: 10.3390/ijms22031259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 01/05/2023] Open
Abstract
Down syndrome (DS) or trisomy of chromosome 21 (Hsa21) is characterized by impaired hippocampal-dependent learning and memory. These alterations are due to defective neurogenesis and to neuromorphological and functional anomalies of numerous neuronal populations, including hippocampal granular cells (GCs). It has been proposed that the additional gene dose in trisomic cells induces modifications in nuclear compartments and on the chromatin landscape, which could contribute to some DS phenotypes. The Ts65Dn (TS) mouse model of DS carries a triplication of 92 genes orthologous to those found in Hsa21, and shares many phenotypes with DS individuals, including cognitive and neuromorphological alterations. Considering its essential role in hippocampal memory formation, we investigated whether the triplication of this set of Hsa21 orthologous genes in TS mice modifies the nuclear architecture of their GCs. Our results show that the TS mouse presents alterations in the nuclear architecture of its GCs, affecting nuclear compartments involved in transcription and pre-rRNA and pre-mRNA processing. In particular, the GCs of the TS mouse show alterations in the nucleolar fusion pattern and the molecular assembly of Cajal bodies (CBs). Furthermore, hippocampal GCs of TS mice present an epigenetic dysregulation of chromatin that results in an increased heterochromatinization and reduced global transcriptional activity. These nuclear alterations could play an important role in the neuromorphological and/or functional alterations of the hippocampal GCs implicated in the cognitive dysfunction characteristic of TS mice.
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Affiliation(s)
- Alba Puente-Bedia
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, 39011 Santander, Spain; (A.P.-B.); (C.M.-C.)
| | - María T. Berciano
- Department of Molecular Biology, “Red sobre Enfermedades Neurodegenerativas (CIBERNED)” and University of Cantabria-IDIVAL, 39011 Santander, Spain;
| | - Olga Tapia
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), “Red sobre Enfermedades Neurodegenerativas (CIBERNED)” and Universidad Europea del Atlántico, 39011 Santander, Spain;
| | - Carmen Martínez-Cué
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, 39011 Santander, Spain; (A.P.-B.); (C.M.-C.)
| | - Miguel Lafarga
- Department of Anatomy and Cell Biology, “Red sobre Enfermedades Neurodegenerativas (CIBERNED)” and University of Cantabria-IDIVAL, 39011 Santander, Spain
- Correspondence: (M.L.); (N.R.); Tel.: +34-942201966 (N.R.); Fax: +34-942201903 (N.R.)
| | - Noemí Rueda
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, 39011 Santander, Spain; (A.P.-B.); (C.M.-C.)
- Correspondence: (M.L.); (N.R.); Tel.: +34-942201966 (N.R.); Fax: +34-942201903 (N.R.)
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6
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Goyani S, Roy M, Singh R. TRIM-NHL as RNA Binding Ubiquitin E3 Ligase (RBUL): Implication in development and disease pathogenesis. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166066. [PMID: 33418035 DOI: 10.1016/j.bbadis.2020.166066] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/14/2020] [Accepted: 12/27/2020] [Indexed: 12/20/2022]
Abstract
TRIM proteins are RING domain-containing modular ubiquitin ligases, unique due to their stimuli specific expression, localization, and turnover. The TRIM family consists of more than 76 proteins, including the TRIM-NHL sub-family which possesses RNA binding ability along with the inherent E3 Ligase activity, hence can be classified as a unique class of RNA Binding Ubiquitin Ligases (RBULs). Having these two abilities, TRIM-NHL proteins can play important role in a wide variety of cellular processes and their dysregulation can lead to complex and systemic pathological conditions. Increasing evidence suggests that TRIM-NHL proteins regulate RNA at the transcriptional and post-transcriptional level having implications in differentiation, development, and many pathological conditions. This review explores the evolving role of TRIM-NHL proteins as TRIM-RBULs, their ubiquitin ligase and RNA binding ability regulating cellular processes, and their possible role in different pathophysiological conditions.
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Affiliation(s)
- Shanikumar Goyani
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, India
| | - Milton Roy
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, India
| | - Rajesh Singh
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, India.
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7
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Zhao L, Li W, Luo X, Sheng S. The multifaceted roles of nucleophagy in cancer development and therapy. Cell Biol Int 2020; 45:246-257. [PMID: 33219602 DOI: 10.1002/cbin.11504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/12/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022]
Abstract
Autophagy is an evolutionarily conserved process in which the cell degrades its own components and recycles the biomolecules for survival and homeostasis. It is an important cellular process to eliminate pathogens or damaged organelles. Nucleophagy, also termed as nuclear autophagy, is a more recently described subtype of autophagy, in which nuclear components, such as nuclear lamina and DNA, are to be degraded. Nucleophagy plays a double-facet role in the development of cancer. On one hand, the clearance of damaged DNA or nuclear structures via autophagic pathway is crucial to maintain nuclear integrity and prevent tumorigenesis. On the other hand, in later stages of tumor growth, nucleophagy may facilitate cancer cell survival and metastasis in the nutrient-depleted microenvironment. In this review, we discuss the relationship between nucleophagy and cancer along with potential intervention methods to target cancer through manipulating nucleophagy. Given the known observations about nucleophagy, it could be promising to target different nuclear components during the processes of nucleophagy, especially nuclear lamina. Further research on investigating the role of nucleophagy in oncological context could focus on dissecting its remaining molecular pathways and their connection to known tumor suppressors.
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Affiliation(s)
- Lili Zhao
- Key Laboratory of Neuroregeneration of Jiangsu, Ministry of Education, Nantong University, Nantong, Jiangsu, China
| | - Wenxi Li
- Northwood High School, Irvine, California, USA.,Department of Oral and Maxillofacial-Head Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xu Luo
- Department of Wounds and Burns, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Surui Sheng
- Department of Oral and Maxillofacial-Head Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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8
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Connacher RP, Goldstrohm AC. Molecular and biological functions of TRIM-NHL RNA-binding proteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1620. [PMID: 32738036 DOI: 10.1002/wrna.1620] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 01/02/2023]
Abstract
The TRIM-NHL family of proteins shares a conserved domain architecture and play crucial roles in stem cell biology, fertility, and development. This review synthesizes new insights that have revolutionized our understanding of the molecular and biological functions of TRIM-NHL proteins. Multiple TRIM-NHLs have been shown to bind specific RNA sequences and structures. X-ray crystal structures of TRIM-NHL proteins in complex with RNA ligands reveal versatile modes of RNA recognition by the NHL domain. Functional and genetic analyses show that TRIM-NHL RNA-binding proteins negatively regulate the protein expression from the target mRNAs that they bind. This repressive activity plays a crucial role in controlling stem cell fate in the developing brain and differentiating germline. To highlight these paradigms, we focus on several of the most-extensively studied TRIM-NHL proteins, specifically Drosophila and vertebrate TRIM71, among others. Brat is essential for development and regulates key target mRNAs to control differentiation of germline and neural stem cells. TRIM71 is also required for development and promotes stem cell proliferation while antagonizing differentiation. Moreover, TRIM71 can be utilized to help reprogram fibroblasts into induced pluripotent stem cells. Recently discovered mutations in TRIM71 cause the neurodevelopmental disease congenital hydrocephalus and emphasize the importance of its RNA-binding function in brain development. Further relevance of TRIM71 to disease pathogenesis comes from evidence linking it to several types of cancer, including liver and testicular cancer. Collectively, these advances demonstrate a primary role for TRIM-NHL proteins in the post-transcriptional regulation of gene expression in crucial biological processes. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Robert P Connacher
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
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9
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Gerisch B, Tharyan RG, Mak J, Denzel SI, Popkes-van Oepen T, Henn N, Antebi A. HLH-30/TFEB Is a Master Regulator of Reproductive Quiescence. Dev Cell 2020; 53:316-329.e5. [PMID: 32302543 DOI: 10.1016/j.devcel.2020.03.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 01/28/2020] [Accepted: 03/15/2020] [Indexed: 12/20/2022]
Abstract
All animals have evolved the ability to survive nutrient deprivation, and nutrient signaling pathways are conserved modulators of health and disease. In C. elegans, late-larval starvation provokes the adult reproductive diapause (ARD), a long-lived quiescent state that enables survival for months without food, yet underlying molecular mechanisms remain unknown. Here, we show that ARD is distinct from other forms of diapause, showing little requirement for canonical longevity pathways, autophagy, and fat metabolism. Instead it requires the HLH-30/TFEB transcription factor to promote the morphological and physiological remodeling involved in ARD entry, survival, and recovery, suggesting that HLH-30 is a master regulator of reproductive quiescence. HLH-30 transcriptome and genetic analyses reveal that Max-like HLH factors, AMP-kinase, mTOR, protein synthesis, and mitochondrial fusion are target processes that promote ARD longevity. ARD thus rewires metabolism to ensure long-term survival and may illuminate similar mechanisms acting in stem cell quiescence and long-term fasting.
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Affiliation(s)
- Birgit Gerisch
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Rebecca George Tharyan
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Jennifer Mak
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Sarah I Denzel
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne 50931, Germany
| | - Till Popkes-van Oepen
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne 50931, Germany
| | - Nadine Henn
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Adam Antebi
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne 50931, Germany.
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10
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Williams FP, Haubrich K, Perez-Borrajero C, Hennig J. Emerging RNA-binding roles in the TRIM family of ubiquitin ligases. Biol Chem 2020; 400:1443-1464. [PMID: 31120853 DOI: 10.1515/hsz-2019-0158] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022]
Abstract
TRIM proteins constitute a large, diverse and ancient protein family which play a key role in processes including cellular differentiation, autophagy, apoptosis, DNA repair, and tumour suppression. Mostly known and studied through the lens of their ubiquitination activity as E3 ligases, it has recently emerged that many of these proteins are involved in direct RNA binding through their NHL or PRY/SPRY domains. We summarise the current knowledge concerning the mechanism of RNA binding by TRIM proteins and its biological role. We discuss how RNA-binding relates to their previously described functions such as E3 ubiquitin ligase activity, and we will consider the potential role of enrichment in membrane-less organelles.
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Affiliation(s)
- Felix Preston Williams
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Kevin Haubrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Cecilia Perez-Borrajero
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany, e-mail:
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11
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Chen PH, Chen YT, Chu TY, Ma TH, Wu MH, Lin HH, Chang YS, Tan BCM, Lo SJ. Nucleolar control by a non-apoptotic p53-caspases-deubiquitinylase axis promotes resistance to bacterial infection. FASEB J 2020; 34:1107-1121. [PMID: 31914708 DOI: 10.1096/fj.201901959r] [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: 08/02/2019] [Revised: 10/02/2019] [Accepted: 10/15/2019] [Indexed: 11/11/2022]
Abstract
The nucleolus is best known for its cellular role in regulating ribosome production and growth. More recently, an unanticipated role for the nucleolus in innate immunity has recently emerged whereby downregulation of fibrillarin and nucleolar contraction confers pathogen resistance across taxa. The mechanism of this downregulation, however, remains obscure. Here we report that rather than fibrillarin itself being the proximal factor in this pathway, the key player is a fibrillarin-stabilizing deubiquitinylase USP-33. This was discovered by a candidate-gene search of Caenorhabditis elegans in which CED-3 caspase was revealed to execute targeted cleavage of USP-33, thus destabilizing fibrillarin. We also showed that cep-1 and ced-3 mutant worms altered nucleolar size and decreased antimicrobial peptide gene, spp-1, expression rendering susceptibility to bacterial infection. These phenotypes were reversed by usp-33 knockdown, thus linking the CEP-1-CED-3-USP-33 pathway with nucleolar control and resistance to bacterial infection in worms. Parallel experiments with the human analogs of caspases and USP36 revealed similar roles in coordinating these two processes. In summary, our work outlined a conserved cascade that connects cell death signaling to nucleolar control and innate immune response.
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Affiliation(s)
- Po-Hsiang Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Tung Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tai-Ying Chu
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Tian-Hsiang Ma
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Mei-Hsuan Wu
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsi-Hsien Lin
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Szecheng J Lo
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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12
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Phan T, Khalid F, Iben S. Nucleolar and Ribosomal Dysfunction-A Common Pathomechanism in Childhood Progerias? Cells 2019; 8:E534. [PMID: 31167386 PMCID: PMC6627804 DOI: 10.3390/cells8060534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/21/2019] [Accepted: 06/02/2019] [Indexed: 01/03/2023] Open
Abstract
The nucleolus organizes around the sites of transcription by RNA polymerase I (RNA Pol I). rDNA transcription by this enzyme is the key step of ribosome biogenesis and most of the assembly and maturation processes of the ribosome occur co-transcriptionally. Therefore, disturbances in rRNA transcription and processing translate to ribosomal malfunction. Nucleolar malfunction has recently been described in the classical progeria of childhood, Hutchinson-Gilford syndrome (HGPS), which is characterized by severe signs of premature aging, including atherosclerosis, alopecia, and osteoporosis. A deregulated ribosomal biogenesis with enlarged nucleoli is not only characteristic for HGPS patients, but it is also found in the fibroblasts of "normal" aging individuals. Cockayne syndrome (CS) is also characterized by signs of premature aging, including the loss of subcutaneous fat, alopecia, and cataracts. It has been shown that all genes in which a mutation causes CS, are involved in rDNA transcription by RNA Pol I. A disturbed ribosomal biogenesis affects mitochondria and translates into ribosomes with a reduced translational fidelity that causes endoplasmic reticulum (ER) stress and apoptosis. Therefore, it is speculated that disease-causing disturbances in the process of ribosomal biogenesis may be more common than hitherto anticipated.
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Affiliation(s)
- Tamara Phan
- Department of Dermatology, Ulm University, James-Franck Ring N27, 89081 Ulm, Germany.
| | - Fatima Khalid
- Department of Dermatology, Ulm University, James-Franck Ring N27, 89081 Ulm, Germany.
| | - Sebastian Iben
- Department of Dermatology, Ulm University, James-Franck Ring N27, 89081 Ulm, Germany.
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13
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Nucleophagy: from homeostasis to disease. Cell Death Differ 2019; 26:630-639. [PMID: 30647432 PMCID: PMC6460388 DOI: 10.1038/s41418-018-0266-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/09/2018] [Accepted: 12/17/2018] [Indexed: 11/08/2022] Open
Abstract
Nuclear abnormalities are prominent in degenerative disease and progeria syndromes. Selective autophagy of organelles is instrumental in maintaining cell homeostasis and prevention of premature ageing. Although the nucleus is the control centre of the cell by safeguarding our genetic material and controlling gene expression, little is known in relation to nuclear autophagy. Here we present recent discoveries in nuclear recycling, namely nucleophagy in physiology in yeast and nucleophagic events that occur in pathological conditions in mammals. The selective nature of degrading nuclear envelope components, DNA, RNA and nucleoli is highlighted. Potential effects of perturbed nucleophagy in senescence and longevity are examined. Moreover, the open questions that remain to be explored are discussed concerning the conditions, receptors and substrates in homeostatic nucleophagy.
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14
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Solis GM, Kardakaris R, Valentine ER, Bar-Peled L, Chen AL, Blewett MM, McCormick MA, Williamson JR, Kennedy B, Cravatt BF, Petrascheck M. Translation attenuation by minocycline enhances longevity and proteostasis in old post-stress-responsive organisms. eLife 2018; 7:40314. [PMID: 30479271 PMCID: PMC6257811 DOI: 10.7554/elife.40314] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/02/2018] [Indexed: 12/12/2022] Open
Abstract
Aging impairs the activation of stress signaling pathways (SSPs), preventing the induction of longevity mechanisms late in life. Here, we show that the antibiotic minocycline increases lifespan and reduces protein aggregation even in old, SSP-deficient Caenorhabditis elegans by targeting cytoplasmic ribosomes, preferentially attenuating translation of highly translated mRNAs. In contrast to most other longevity paradigms, minocycline inhibits rather than activates all major SSPs and extends lifespan in mutants deficient in the activation of SSPs, lysosomal or autophagic pathways. We propose that minocycline lowers the concentration of newly synthesized aggregation-prone proteins, resulting in a relative increase in protein-folding capacity without the necessity to induce protein-folding pathways. Our study suggests that in old individuals with incapacitated SSPs or autophagic pathways, pharmacological attenuation of cytoplasmic translation is a promising strategy to reduce protein aggregation. Altogether, it provides a geroprotecive mechanism for the many beneficial effects of tetracyclines in models of neurodegenerative disease. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Gregory M Solis
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,Department of Neuroscience, The Scripps Research Institute, La Jolla, United States
| | - Rozina Kardakaris
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States
| | - Elizabeth R Valentine
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Liron Bar-Peled
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Alice L Chen
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Megan M Blewett
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | | | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Brian Kennedy
- The Buck Institute for Research on Aging, Novato, United States
| | - Benjamin F Cravatt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Michael Petrascheck
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,Department of Neuroscience, The Scripps Research Institute, La Jolla, United States
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15
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Tiku V, Kew C, Mehrotra P, Ganesan R, Robinson N, Antebi A. Nucleolar fibrillarin is an evolutionarily conserved regulator of bacterial pathogen resistance. Nat Commun 2018; 9:3607. [PMID: 30190478 PMCID: PMC6127302 DOI: 10.1038/s41467-018-06051-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 07/19/2018] [Indexed: 02/04/2023] Open
Abstract
Innate immunity is the first line of defense against infections. Pathways regulating innate responses can also modulate other processes, including stress resistance and longevity. Increasing evidence suggests a role for the nucleolus in regulating cellular processes implicated in health and disease. Here we show the highly conserved nucleolar protein, fibrillarin, is a vital factor regulating pathogen resistance. Fibrillarin knockdown enhances resistance in C. elegans against bacterial pathogens, higher levels of fibrillarin induce susceptibility to infection. Pathogenic infection reduces nucleolar size, ribsosomal RNA, and fibrillarin levels. Genetic epistasis reveals fibrillarin functions independently of the major innate immunity mediators, suggesting novel mechanisms of pathogen resistance. Bacterial infection also reduces nucleolar size and fibrillarin levels in mammalian cells. Fibrillarin knockdown prior to infection increases intracellular bacterial clearance, reduces inflammation, and enhances cell survival. Collectively, these findings reveal an evolutionarily conserved role of fibrillarin in infection resistance and suggest the nucleolus as a focal point in innate immune responses.
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Affiliation(s)
- Varnesh Tiku
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany.,Department of Infectious Diseases, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Chun Kew
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931, Cologne, Germany
| | - Parul Mehrotra
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931, Cologne, Germany.,VIB-Center for Inflammation Research, VIB - Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Raja Ganesan
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, 50674, Cologne, Germany
| | - Nirmal Robinson
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany. .,Centre for Cancer Biology, University of South Australia, HB11-35 UniSA CRI Building, North Terrace, 5001, Adelaide, Australia.
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931, Cologne, Germany. .,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany.
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16
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Arias Escayola D, Neugebauer KM. Dynamics and Function of Nuclear Bodies during Embryogenesis. Biochemistry 2018; 57:2462-2469. [PMID: 29473743 DOI: 10.1021/acs.biochem.7b01262] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Nuclear bodies are RNA-rich membraneless organelles in the cell nucleus that concentrate specific sets of nuclear proteins and RNA-protein complexes. Nuclear bodies such as the nucleolus, Cajal body (CB), and the histone locus body (HLB) concentrate factors required for nuclear steps of RNA processing. Formation of these nuclear bodies occurs on genomic loci and is frequently associated with active sites of transcription. Whether nuclear body formation is dependent on a particular gene element, an active process such as transcription, or the nascent RNA present at gene loci is a topic of debate. Recently, this question has been addressed through studies in model organisms and their embryos. The switch from maternally provided RNA and protein to zygotic gene products in early embryos has been well characterized in a variety of organisms. This process, termed maternal-to-zygotic transition, provides an excellent model for studying formation of nuclear bodies before, during, and after the transcriptional activation of the zygotic genome. Here, we review findings in embryos that reveal key principles in the study of the formation and function of nucleoli, CBs, and HLBs. We propose that while particular gene elements may contribute to formation of these nuclear bodies, active transcription promotes maturation of nuclear bodies and efficient RNA processing within them.
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Affiliation(s)
- Dahyana Arias Escayola
- Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520-8114 , United States
| | - Karla M Neugebauer
- Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520-8114 , United States
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17
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West SM, Mecenas D, Gutwein M, Aristizábal-Corrales D, Piano F, Gunsalus KC. Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline. Genome Biol 2018; 19:8. [PMID: 29368663 PMCID: PMC5784609 DOI: 10.1186/s13059-017-1369-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 12/03/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The 3' untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produces multiple transcript isoforms for the same gene within and across different cell types. Using LITE-Seq, a new quantitative method to capture transcript 3' ends expressed in vivo, we have characterized sex- and cell type-specific transcriptome-wide changes in gene expression and 3'UTR diversity in Caenorhabditis elegans germline cells undergoing proliferation and differentiation. RESULTS We show that nearly half of germline transcripts are alternatively polyadenylated, that differential regulation of endogenous 3'UTR variants is common, and that alternative isoforms direct distinct spatiotemporal protein expression patterns in vivo. Dynamic expression profiling also reveals temporal regulation of X-linked gene expression, selective stabilization of transcripts, and strong evidence for a novel developmental program that promotes nucleolar dissolution in oocytes. We show that the RNA-binding protein NCL-1/Brat is a posttranscriptional regulator of numerous ribosome-related transcripts that acts through specific U-rich binding motifs to down-regulate mRNAs encoding ribosomal protein subunits, rRNA processing factors, and tRNA synthetases. CONCLUSIONS These results highlight the pervasive nature and functional potential of patterned gene and isoform expression during early animal development.
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Affiliation(s)
- Sean M West
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Desirea Mecenas
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Michelle Gutwein
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - David Aristizábal-Corrales
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Fabio Piano
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA.
- Center for Genomics & Systems Biology, NYU Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
| | - Kristin C Gunsalus
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA.
- Center for Genomics & Systems Biology, NYU Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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18
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Hierarchical Size Scaling during Multicellular Growth and Development. Cell Rep 2017; 17:345-352. [PMID: 27705784 DOI: 10.1016/j.celrep.2016.09.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/12/2016] [Accepted: 09/01/2016] [Indexed: 01/09/2023] Open
Abstract
Multicellular organisms must regulate their growth across the diverse length scales of biological organization, but how this growth is controlled from organelle to body, while coordinating interdependent functions at each scale, remains poorly understood. We utilized the C. elegans worm intestine as a model system to identify distinct allometric scaling laws, revealing that the growth of individual structures is differentially regulated during development. We show that the volume of the nucleolus, a subcellular organelle, is directly proportional (isometric) to cell size during larval development. In contrast to findings in a variety of other systems, the size of the nucleus grows more slowly and is hypoallometric to the cell. We further demonstrate that the relative size of the nucleolus, the site of ribosome biogenesis, is predictive of the growth rate of the entire worm. These results highlight the importance of subcellular size for organism-level function in multicellular organisms.
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19
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Tiku V, Jain C, Raz Y, Nakamura S, Heestand B, Liu W, Späth M, Suchiman HED, Müller RU, Slagboom PE, Partridge L, Antebi A. Small nucleoli are a cellular hallmark of longevity. Nat Commun 2017; 8:16083. [PMID: 28853436 PMCID: PMC5582349 DOI: 10.1038/ncomms16083] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 05/26/2017] [Indexed: 12/21/2022] Open
Abstract
Animal lifespan is regulated by conserved metabolic signalling pathways and specific transcription factors, but whether these pathways affect common downstream mechanisms remains largely elusive. Here we show that NCL-1/TRIM2/Brat tumour suppressor extends lifespan and limits nucleolar size in the major C. elegans longevity pathways, as part of a convergent mechanism focused on the nucleolus. Long-lived animals representing distinct longevity pathways exhibit small nucleoli, and decreased expression of rRNA, ribosomal proteins, and the nucleolar protein fibrillarin, dependent on NCL-1. Knockdown of fibrillarin also reduces nucleolar size and extends lifespan. Among wildtype C. elegans, individual nucleolar size varies, but is highly predictive for longevity. Long-lived dietary restricted fruit flies and insulin-like-peptide mutants exhibit small nucleoli and fibrillarin expression, as do long-lived dietary restricted and IRS1 knockout mice. Furthermore, human muscle biopsies from individuals who underwent modest dietary restriction coupled with exercise also display small nucleoli. We suggest that small nucleoli are a cellular hallmark of longevity and metabolic health conserved across taxa. Animal lifespan is plastic and is regulated by conserved signalling pathways. Here, Tiku et al. show that longevity-enhancing mutations or interventions are associated with reduced nucleolar size in worms, flies, mice and humans, and that nucleolar size can predict life-expectancy in individual worms.
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Affiliation(s)
- Varnesh Tiku
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674 Cologne, Germany
| | - Chirag Jain
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany
| | - Yotam Raz
- Section of Molecular Epidemiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Shuhei Nakamura
- Department of Genetics, Graduate School of Medicine, Osaka University 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Bree Heestand
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-3280, USA
| | - Wei Liu
- Department of Molecular and Cellular Biology, Huffington Center on Aging, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Martin Späth
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674 Cologne, Germany
| | - H Eka D Suchiman
- Section of Molecular Epidemiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Roman-Ulrich Müller
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674 Cologne, Germany.,Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, 50674 Cologne, Germany
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Linda Partridge
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674 Cologne, Germany
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674 Cologne, Germany
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20
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Cohen-Fix O, Askjaer P. Cell Biology of the Caenorhabditis elegans Nucleus. Genetics 2017; 205:25-59. [PMID: 28049702 PMCID: PMC5216270 DOI: 10.1534/genetics.116.197160] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/09/2016] [Indexed: 12/25/2022] Open
Abstract
Studies on the Caenorhabditis elegans nucleus have provided fascinating insight to the organization and activities of eukaryotic cells. Being the organelle that holds the genetic blueprint of the cell, the nucleus is critical for basically every aspect of cell biology. The stereotypical development of C. elegans from a one cell-stage embryo to a fertile hermaphrodite with 959 somatic nuclei has allowed the identification of mutants with specific alterations in gene expression programs, nuclear morphology, or nuclear positioning. Moreover, the early C. elegans embryo is an excellent model to dissect the mitotic processes of nuclear disassembly and reformation with high spatiotemporal resolution. We review here several features of the C. elegans nucleus, including its composition, structure, and dynamics. We also discuss the spatial organization of chromatin and regulation of gene expression and how this depends on tight control of nucleocytoplasmic transport. Finally, the extensive connections of the nucleus with the cytoskeleton and their implications during development are described. Most processes of the C. elegans nucleus are evolutionarily conserved, highlighting the relevance of this powerful and versatile model organism to human biology.
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Affiliation(s)
- Orna Cohen-Fix
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Peter Askjaer
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
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21
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22
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Feric M, Vaidya N, Harmon TS, Mitrea DM, Zhu L, Richardson TM, Kriwacki RW, Pappu RV, Brangwynne CP. Coexisting Liquid Phases Underlie Nucleolar Subcompartments. Cell 2016; 165:1686-1697. [PMID: 27212236 DOI: 10.1016/j.cell.2016.04.047] [Citation(s) in RCA: 1162] [Impact Index Per Article: 145.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/11/2016] [Accepted: 04/13/2016] [Indexed: 12/26/2022]
Abstract
The nucleolus and other ribonucleoprotein (RNP) bodies are membrane-less organelles that appear to assemble through phase separation of their molecular components. However, many such RNP bodies contain internal subcompartments, and the mechanism of their formation remains unclear. Here, we combine in vivo and in vitro studies, together with computational modeling, to show that subcompartments within the nucleolus represent distinct, coexisting liquid phases. Consistent with their in vivo immiscibility, purified nucleolar proteins phase separate into droplets containing distinct non-coalescing phases that are remarkably similar to nucleoli in vivo. This layered droplet organization is caused by differences in the biophysical properties of the phases-particularly droplet surface tension-which arises from sequence-encoded features of their macromolecular components. These results suggest that phase separation can give rise to multilayered liquids that may facilitate sequential RNA processing reactions in a variety of RNP bodies. PAPERCLIP.
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Affiliation(s)
- Marina Feric
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Nilesh Vaidya
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Tyler S Harmon
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Lian Zhu
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Tiffany M Richardson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
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23
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Sheng M, Gorzsás A, Tuck S. Fourier transform infrared microspectroscopy for the analysis of the biochemical composition of C. elegans worms. WORM 2016; 5:e1132978. [PMID: 27073735 DOI: 10.1080/21624054.2015.1132978] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/07/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Changes in intermediary metabolism have profound effects on many aspects of C. elegans biology including growth, development and behavior. However, many traditional biochemical techniques for analyzing chemical composition require relatively large amounts of starting material precluding the analysis of mutants that cannot be grown in large amounts as homozygotes. Here we describe a technique for detecting changes in the chemical compositions of C. elegans worms by Fourier transform infrared microspectroscopy. We demonstrate that the technique can be used to detect changes in the relative levels of carbohydrates, proteins and lipids in one and the same worm. We suggest that Fourier transform infrared microspectroscopy represents a useful addition to the arsenal of techniques for metabolic studies of C. elegans worms.
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Affiliation(s)
- Ming Sheng
- Umeå Center for Molecular Medicine, Umeå University , Umeå, Sweden
| | | | - Simon Tuck
- Umeå Center for Molecular Medicine, Umeå University , Umeå, Sweden
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24
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Ma TH, Lee LW, Lee CC, Yi YH, Chan SP, Tan BCM, Lo SJ. Genetic control of nucleolar size: An evolutionary perspective. Nucleus 2016; 7:112-20. [PMID: 27003693 DOI: 10.1080/19491034.2016.1166322] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Exploiting a C. elegans mutant (ncl-1) exhibiting nucleolar abnormalities, we recently identified the let-7/ncl-1/fib-1 genetic cascade underlying proper rRNA abundance and nucleolar size. These 3 factors, let-7 (a miRNA), NCL-1 (a member of the TRIM-NHL family), and fibrillarin (a nucleolar methyltransferase), are evolutionarily conserved across metazoans. In this article, we provide several lines of bioinformatic evidence showing that human and Drosophila homologues of C. elegans NCL-1, TRIM-71 and Brat, respectively, likely act as translational suppressors of fibrillarin. Moreover, since their 3'-UTRs contain putative target sites, they may also be under the control of the let-7 miRNA. We hypothesize that let-7, TRIM and fibrillarin contribute activities in concert, and constitute a conserved network controlling nucleolar size in eukaryotes. We provide an in-depth literature review of various molecular pathways, including the let-7/ncl-1/fib-1 genetic cascade, implicated in the regulation of nucleolar size.
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Affiliation(s)
- Tian-Hsiang Ma
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Li-Wei Lee
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Chi-Chang Lee
- d Institute of Chemistry , Academia Sinica , Taipei , Taiwan
| | - Yung-Hsiang Yi
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Shih-Peng Chan
- e Graduate Institute of Microbiology , College of Medicine , National Taiwan University , Taipei , Taiwan
| | - Bertrand Chin-Ming Tan
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Szecheng J Lo
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
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Abstract
TRIM-NHL proteins are key regulators of developmental transitions, for example promoting differentiation, while inhibiting cell growth and proliferation, in stem and progenitor cells. Abnormalities in these proteins have been also associated with human diseases, particularly affecting muscular and neuronal functions, making them potential targets for therapeutic intervention. The purpose of this review is to provide a systematic and comprehensive summary on the most studied TRIM-NHL proteins, highlighting examples where connections were established between structural features, molecular functions and biological outcomes.
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Affiliation(s)
- Cristina Tocchini
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Rafal Ciosk
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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26
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de Lucas MP, Sáez AG, Lozano E. miR-58 family and TGF-β pathways regulate each other in Caenorhabditis elegans. Nucleic Acids Res 2015; 43:9978-93. [PMID: 26400166 PMCID: PMC4783514 DOI: 10.1093/nar/gkv923] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 08/14/2015] [Accepted: 09/07/2015] [Indexed: 12/19/2022] Open
Abstract
Despite the fact that microRNAs (miRNAs) modulate the expression of around 60% of protein-coding genes, it is often hard to elucidate their precise role and target genes. Studying miRNA families as opposed to single miRNAs alone increases our chances of observing not only mutant phenotypes but also changes in the expression of target genes. Here we ask whether the TGF-β signalling pathways, which control many animal processes, might be modulated by miRNAs in Caenorhabditis elegans. Using a mutant for four members of the mir-58 family, we show that both TGF-β Sma/Mab (controlling body size) and TGF-β Dauer (regulating dauer, a stress-resistant larval stage) are upregulated. Thus, mir-58 family directly inhibits the expression of dbl-1 (ligand), daf-1, daf-4 and sma-6 (receptors) of TGF-β pathways. Epistasis experiments reveal that whereas the small body phenotype of the mir-58 family mutant must invoke unknown targets independent from TGF-β Sma/Mab, its dauer defectiveness can be rescued by DAF-1 depletion. Additionally, we found a negative feedback loop between TGF-β Sma/Mab and mir-58 and the related mir-80. Our results suggest that the interaction between mir-58 family and TGF-β genes is key on decisions about animal growth and stress resistance in C. elegans and perhaps other organisms.
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Affiliation(s)
- María Pilar de Lucas
- Unidad Funcional de Investigación de Enfermedades Crónicas, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Alberto G Sáez
- Unidad Funcional de Investigación de Enfermedades Crónicas, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Encarnación Lozano
- Unidad Funcional de Investigación de Enfermedades Crónicas, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
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27
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Yi YH, Ma TH, Lee LW, Chiou PT, Chen PH, Lee CM, Chu YD, Yu H, Hsiung KC, Tsai YT, Lee CC, Chang YS, Chan SP, Tan BCM, Lo SJ. A Genetic Cascade of let-7-ncl-1-fib-1 Modulates Nucleolar Size and rRNA Pool in Caenorhabditis elegans. PLoS Genet 2015; 11:e1005580. [PMID: 26492166 PMCID: PMC4619655 DOI: 10.1371/journal.pgen.1005580] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/15/2015] [Indexed: 11/20/2022] Open
Abstract
Ribosome biogenesis takes place in the nucleolus, the size of which is often coordinated with cell growth and development. However, how metazoans control nucleolar size remains largely unknown. Caenorhabditis elegans provides a good model to address this question owing to distinct tissue distribution of nucleolar sizes and a mutant, ncl-1, which exhibits larger nucleoli than wild-type worms. Here, through a series of loss-of-function analyses, we report that the nucleolar size is regulated by a circuitry composed of microRNA let-7, translation repressor NCL-1, and a major nucleolar pre-rRNA processing protein FIB-1/fibrillarin. In cooperation with RNA binding proteins PUF and NOS, NCL-1 suppressed the translation of FIB-1/fibrillarin, while let-7 targeted the 3’UTR of ncl-1 and inhibited its expression. Consequently, the abundance of FIB-1 is tightly controlled and correlated with the nucleolar size. Together, our findings highlight a novel genetic cascade by which post-transcriptional regulators interplay in developmental control of nucleolar size and function. Among the RNA/protein bodies within the nucleus, nucleoli are essential factories for ribosome production and assembly. The size and morphology of the nucleolus is thus a cytological manifestation of protein biosynthesis and is closely coordinated with cell biology and even malignancy. However, without membrane delimitation, the principles that define nucleoli size are poorly understood. Caenorhabditis elegans represents an ideal model to address this question owing to distinct tissue distribution of nucleolar sizes and a mutant, ncl-1, which exhibits larger-than-normal nucleoli. We report here a genetic cascade of microRNA let-7 and translation repressor NCL-1, which tightly controls abundance of FIB-1/fibrillarin. This network ultimately contributes to developmental control of nucleolar size and function.
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Affiliation(s)
- Yung-Hsiang Yi
- Molecular Medicine Research Center, Chang Gung University, TaoYuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Tian-Hsiang Ma
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Li-Wei Lee
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Pey-Tsyr Chiou
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Po-Hsiang Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Ching-Ming Lee
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Yu-De Chu
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsiang Yu
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Kuei-Ching Hsiung
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Yi-Tzang Tsai
- Molecular Medicine Research Center, Chang Gung University, TaoYuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Chi-Chang Lee
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, TaoYuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Shih-Peng Chan
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- * E-mail: (SPC); (BCMT); (SJL)
| | - Bertrand Chin-Ming Tan
- Molecular Medicine Research Center, Chang Gung University, TaoYuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
- * E-mail: (SPC); (BCMT); (SJL)
| | - Szecheng J. Lo
- Molecular Medicine Research Center, Chang Gung University, TaoYuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, TaoYuan, Taiwan
- * E-mail: (SPC); (BCMT); (SJL)
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28
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Weber SC, Brangwynne CP. Inverse size scaling of the nucleolus by a concentration-dependent phase transition. Curr Biol 2015; 25:641-6. [PMID: 25702583 DOI: 10.1016/j.cub.2015.01.012] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 12/03/2014] [Accepted: 01/05/2015] [Indexed: 10/24/2022]
Abstract
Just as organ size typically increases with body size, the size of intracellular structures changes as cells grow and divide. Indeed, many organelles, such as the nucleus [1, 2], mitochondria [3], mitotic spindle [4, 5], and centrosome [6], exhibit size scaling, a phenomenon in which organelle size depends linearly on cell size. However, the mechanisms of organelle size scaling remain unclear. Here, we show that the size of the nucleolus, a membraneless organelle important for cell-size homeostasis [7], is coupled to cell size by an intracellular phase transition. We find that nucleolar size directly scales with cell size in early C. elegans embryos. Surprisingly, however, when embryo size is altered, we observe inverse scaling: nucleolar size increases in small cells and decreases in large cells. We demonstrate that this seemingly contradictory result arises from maternal loading of a fixed number rather than a fixed concentration of nucleolar components, which condense into nucleoli only above a threshold concentration. Our results suggest that the physics of phase transitions can dictate whether an organelle assembles, and, if so, its size, providing a mechanistic link between organelle assembly and cell size. Since the nucleolus is known to play a key role in cell growth, this biophysical readout of cell size could provide a novel feedback mechanism for growth control.
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Affiliation(s)
- Stephanie C Weber
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
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29
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Tuck S. The control of cell growth and body size in Caenorhabditis elegans. Exp Cell Res 2013; 321:71-6. [PMID: 24262077 DOI: 10.1016/j.yexcr.2013.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/08/2013] [Accepted: 11/11/2013] [Indexed: 01/02/2023]
Abstract
One of the most important ways in which animal species vary is in their size. Individuals of the largest animal ever thought to have lived, the blue whale (Balaenoptera musculus), can reach a weight of 190 t and a length of over 30 m. At the other extreme, among the smallest multicellular animals are males of the parasitic wasp, Dicopomorpha echmepterygis, which even as adults are just 140 μm in length. In terms of volume, these species differ by more than 14 orders of magnitude. Since size has such profound effects on an organism's ecology, anatomy and physiology, an important task for evolutionary biology and ecology is to account for why organisms grow to their characteristic sizes. Equally, a full description of an organism's development must include an explanation of how its growth and body size are regulated. Here I review research on how these processes are controlled in the nematode, Caenorhabditis elegans. Analyses of small and long mutants have revealed that in the worm, DBL-1, a ligand in the TGFβ superfamily family, promotes growth in a dose-dependent manner. DBL-1 signaling affects body size by stimulating the growth of syncytial hypodermal cells rather than controlling cell division. Signals from chemosensory neurons and from the gonad also modulate body size, in part, independently of DBL-1-mediated signaling. Organismal size and morphology is heavily influenced by the cuticle, which acts as the exoskeleton. Finally, I summarize research on several genes that appear to regulate body size by cell autonomously regulating cell growth throughout the worm.
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Affiliation(s)
- Simon Tuck
- Umeå Center for Molecular Medicine, Umeå University, SE-901 87 Umeå, Sweden.
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30
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Kihira S, Yu EJ, Cunningham J, Cram EJ, Lee M. A novel mutation in β integrin reveals an integrin-mediated interaction between the extracellular matrix and cki-1/p27KIP1. PLoS One 2012; 7:e42425. [PMID: 22879977 PMCID: PMC3412830 DOI: 10.1371/journal.pone.0042425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 07/09/2012] [Indexed: 01/20/2023] Open
Abstract
The cell-extracellular matrix (ECM) interaction plays an essential role in maintaining tissue shapes and regulates cell behaviors such as cell adhesion, differentiation and proliferation. The mechanism by which the ECM influences the cell cycle in vivo is poorly understood. Here we demonstrate that the β integrin PAT-3 regulates the localization and expression of CKI-1, a C. elegans homologue of the cyclin dependent kinase inhibitor p27(KIP1). In nematodes expressing wild type PAT-3, CKI-1::GFP localizes primarily to nucleoli in hypodermal cells, whereas in animals expressing mutant pat-3 with a defective splice junction, CKI-1::GFP appears clumped and disorganized in nucleoplasm. RNAi analysis links cell adhesion genes to the regulation of CKI-1. RNAi of unc-52/perlecan, ina-1/α integrin, pat-4/ILK, and unc-97/PINCH resulted in abnormal CKI-1::GFP localization. Additional RNAi experiments revealed that the SCF E3 ubiquitin-ligase complex genes, skpt-1/SKP2, cul-1/CUL1 and lin-23/F-box, are required for the proper localization and expression of CKI-1, suggesting that integrin signaling and SCF E3 ligase work together to regulate the cellular distribution of CKI-1. These data also suggest that integrin plays a major role in maintaining proper CKI-1/p27(KIP1) levels in the cell. Perturbed integrin signaling may lead to the inhibition of SCF ligase activity, mislocalization and elevation of CKI-1/p27(KIP1). These results suggest that adhesion signaling is crucial for cell cycle regulation in vivo.
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Affiliation(s)
- Shingo Kihira
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Eun Jeong Yu
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jessica Cunningham
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Erin J. Cram
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Myeongwoo Lee
- Department of Biology, Baylor University, Waco, Texas, United States of America
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31
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Abstract
In the Caenorhabditis elegans nematode, the oocyte nucleolus disappears prior to fertilization. We have now investigated the re-formation of the nucleolus in the early embryo of this model organism by immunostaining for fibrillarin and DAO-5, a putative NOLC1/Nopp140 homolog involved in ribosome assembly. We find that labeled nucleoli first appear in somatic cells at around the 8-cell stage, at a time when transcription of the embryonic genome begins. Quantitative analysis of radial positioning showed the nucleolus to be localized at the nuclear periphery in a majority of early embryonic nuclei. At the ultrastructural level, the embryonic nucleolus appears to be composed of a relatively homogenous core surrounded by a crescent-shaped granular structure. Prior to embryonic genome activation, fibrillarin and DAO-5 staining is seen in numerous small nucleoplasmic foci. This staining pattern persists in the germline up to the ∼100-cell stage, until the P4 germ cell divides to give rise to the Z2/Z3 primordial germ cells and embryonic transcription is activated in this lineage. In the ncl-1 mutant, which is characterized by increased transcription of rDNA, DAO-5-labeled nucleoli are already present at the 2-cell stage. Our results suggest a link between the activation of transcription and the initial formation of nucleoli in the C. elegans embryo.
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32
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The nucleolus of Caenorhabditis elegans. J Biomed Biotechnol 2012; 2012:601274. [PMID: 22577294 PMCID: PMC3345250 DOI: 10.1155/2012/601274] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 12/15/2011] [Accepted: 01/09/2012] [Indexed: 12/31/2022] Open
Abstract
Nucleolar size and appearance correlate with ribosome biogenesis and cellular activity. The mechanisms underlying changes in nucleolar appearance and regulation of nucleolar size that occur during differentiation and cell cycle progression are not well understood. Caenorhabditis elegans provides a good model for studying these processes because of its small size and transparent body, well-characterized cell types and lineages, and because its cells display various sizes of nucleoli. This paper details the advantages of using C. elegans to investigate features of the nucleolus during the organism's development by following dynamic changes in fibrillarin (FIB-1) in the cells of early embryos and aged worms. This paper also illustrates the involvement of the ncl-1 gene and other possible candidate genes in nucleolar-size control. Lastly, we summarize the ribosomal proteins involved in life span and innate immunity, and those homologous genes that correspond to human disorders of ribosomopathy.
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33
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Abstract
Some members of the tripartite motif (TRIM/RBCC) protein family are thought to be important regulators of carcinogenesis. This is not surprising as the TRIM proteins are involved in several biological processes, such as cell growth, development and cellular differentiation and alteration of these proteins can affect transcriptional regulation, cell proliferation and apoptosis. In particular, four TRIM family genes are frequently translocated to other genes, generating fusion proteins implicated in cancer initiation and progression. Among these the most famous is the promyelocytic leukaemia gene PML, which encodes the protein TRIM19. PML is involved in the t(15;17) translocation that specifically occurs in Acute Promyelocytic Leukaemia (APL), resulting in a PML-retinoic acid receptor-alpha (PML-RARalpha) fusion protein. Other members of the TRIM family are linked to cancer development without being involved in chromosomal re-arrangements, possibly through ubiquitination or loss of tumour suppression functions. This chapter discusses the biological functions of TRIM proteins in cancer.
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34
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Chi YH, Ahn JE, Yun DJ, Lee SY, Liu TX, Zhu-Salzman K. Changes in oxygen and carbon dioxide environment alter gene expression of cowpea bruchids. JOURNAL OF INSECT PHYSIOLOGY 2011; 57:220-230. [PMID: 21078326 DOI: 10.1016/j.jinsphys.2010.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 11/05/2010] [Accepted: 11/08/2010] [Indexed: 05/30/2023]
Abstract
Hermetic storage is a widely adopted technique for preventing stored grain from being damaged by storage insect pests. In the air-tight container, insects consume oxygen through metabolism while concomitantly raising carbon dioxide concentrations through respiration. Previous studies on the impact of hypoxia and hypercapnia on feeding behavior of cowpea bruchids have shown that feeding activity gradually decreases in proportion to the changing gas concentrations and virtually ceases at approximately 3-6% (v/v) oxygen and 15-18% carbon dioxide. Further, a number of bruchid larvae are able to recover their feeding activity after days of low oxygen and high carbon dioxide, although extended exposure tends to reduce survival. In the current study, to gain insight into the molecular mechanism underpinning the hypoxia-coping response, we profiled transcriptomic responses to hypoxia/hypercapnia (3% oxygen, 17% carbon dioxide for 4 and 24h) using cDNA microarrays, followed by quantitative RT-PCR verification of selected gene expression changes. A total of 1046 hypoxia-responsive cDNAs were sequenced; these clustered into 765 contigs, of which 645 were singletons. Many (392) did not show homology with known genes, or had homology only with genes of unknown function in a BLAST search. The identified differentially-regulated sequences encoded proteins presumptively involved in nutrient transport and metabolism, cellular signaling and structure, development, and stress responses. Gene expression profiles suggested that insects compensate for lack of oxygen by coordinately reducing energy demand, shifting to anaerobic metabolism, and strengthening cellular structure and muscular contraction.
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Affiliation(s)
- Yong Hun Chi
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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35
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Goldsmith AD, Sarin S, Lockery S, Hobert O. Developmental control of lateralized neuron size in the nematode Caenorhabditis elegans. Neural Dev 2010; 5:33. [PMID: 21122110 PMCID: PMC3014911 DOI: 10.1186/1749-8104-5-33] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 12/01/2010] [Indexed: 01/11/2023] Open
Abstract
Background Nervous systems are generally bilaterally symmetric on a gross structural and organizational level but are strongly lateralized (left/right asymmetric) on a functional level. It has been previously noted that in vertebrate nervous systems, symmetrically positioned, bilateral groups of neurons in functionally lateralized brain regions differ in the size of their soma. The genetic mechanisms that control these left/right asymmetric soma size differences are unknown. The nematode Caenorhabditis elegans offers the opportunity to study this question with single neuron resolution. A pair of chemosensory neurons (ASEL and ASER), which are bilaterally symmetric on several levels (projections, synaptic connectivity, gene expression patterns), are functionally lateralized in that they express distinct chemoreceptors and sense distinct chemosensory cues. Results We describe here that ASEL and ASER also differ substantially in size (soma volume, axonal and dendritic diameter), a feature that is predicted to change the voltage conduction properties of the two sensory neurons. This difference in size is not dependent on sensory input or neuronal activity but developmentally programmed by a pathway of gene regulatory factors that also control left/right asymmetric chemoreceptor expression of the two ASE neurons. This regulatory pathway funnels via the DIE-1 Zn finger transcription factor into the left/right asymmetric distribution of nucleoli that contain the rRNA regulator Fibrillarin/FIB-1, a RNA methyltransferase implicated in the non-hereditary immune disease scleroderma, which we find to be essential to establish the size differences between ASEL and ASER. Conclusions Taken together, our findings reveal a remarkable conservation of the linkage of functional lateralization with size differences across phylogeny and provide the first insights into the developmentally programmed regulatory mechanisms that control neuron size lateralities.
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Affiliation(s)
- Andrew D Goldsmith
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
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36
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Wenemoser D, Reddien PW. Planarian regeneration involves distinct stem cell responses to wounds and tissue absence. Dev Biol 2010; 344:979-91. [PMID: 20599901 DOI: 10.1016/j.ydbio.2010.06.017] [Citation(s) in RCA: 225] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 06/11/2010] [Indexed: 10/19/2022]
Abstract
Regeneration requires signaling from a wound site for detection of the wound and a mechanism that determines the nature of the injury to specify the appropriate regenerative response. Wound signals and tissue responses to wounds that elicit regeneration remain poorly understood. Planarians are able to regenerate from essentially any type of injury and present a novel system for the study of wound responses in regeneration initiation. Newly developed molecular and cellular tools now enable study of regeneration initiation using the planarian Schmidtea mediterranea. Planarian regeneration requires adult stem cells called neoblasts and amputation triggers two peaks in neoblast mitoses early in regeneration. We demonstrate that the first mitotic peak is a body-wide response to any injury and that a second, local, neoblast response is induced only when injury results in missing tissue. This second response was characterized by recruitment of neoblasts to wounds, even in areas that lack neoblasts in the intact animal. Subsequently, these neoblasts were induced to divide and differentiate near the wound, leading to formation of new tissue. We conclude that there exist two functionally distinct signaling phases of the stem cell wound response that distinguish between simple injury and situations that require the regeneration of missing tissue.
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Affiliation(s)
- Danielle Wenemoser
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, USA
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37
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Hwang SY, Rose LS. Control of asymmetric cell division in early C. elegans embryogenesis: teaming-up translational repression and protein degradation. BMB Rep 2010; 43:69-78. [PMID: 20193124 DOI: 10.5483/bmbrep.2010.43.2.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Asymmetric cell division is a fundamental mechanism for the generation of body axes and cell diversity during early embryogenesis in many organisms. During intrinsically asymmetric divisions, an axis of polarity is established within the cell and the division plane is oriented to ensure the differential segregation of developmental determinants to the daughter cells. Studies in the nematode Caenorhabditis elegans have contributed greatly to our understanding of the regulatory mechanisms underlying cell polarity and asymmetric division. However, much remains to be elucidated about the molecular machinery controlling the spatiotemporal distribution of key components. In this review we discuss recent findings that reveal intricate interactions between translational control and targeted proteolysis. These two mechanisms of regulation serve to carefully modulate protein levels and reinforce asymmetries, or to eliminate proteins from certain cells.
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Affiliation(s)
- Sue-Yun Hwang
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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38
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Neumüller RA, Knoblich JA. Dividing cellular asymmetry: asymmetric cell division and its implications for stem cells and cancer. Genes Dev 2009; 23:2675-99. [PMID: 19952104 DOI: 10.1101/gad.1850809] [Citation(s) in RCA: 297] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cell division is commonly thought to involve the equal distribution of cellular components into the two daughter cells. During many cell divisions, however, proteins, membrane compartments, organelles, or even DNA are asymmetrically distributed between the two daughter cells. Here, we review the various types of asymmetries that have been described in yeast and in animal cells. Asymmetric segregation of protein determinants is particularly relevant for stem cell biology. We summarize the relevance of asymmetric cell divisions in various stem cell systems and discuss why defects in asymmetric cell division can lead to the formation of tumors.
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Affiliation(s)
- Ralph A Neumüller
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
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C. elegans nucleostemin is required for larval growth and germline stem cell division. PLoS Genet 2008; 4:e1000181. [PMID: 18725931 PMCID: PMC2515194 DOI: 10.1371/journal.pgen.1000181] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 07/22/2008] [Indexed: 11/25/2022] Open
Abstract
The nucleolus has shown to be integral for many processes related to cell growth and proliferation. Stem cells in particular are likely to depend upon nucleolus-based processes to remain in a proliferative state. A highly conserved nucleolar factor named nucleostemin is proposed to be a critical link between nucleolar function and stem-cell–specific processes. Currently, it is unclear whether nucleostemin modulates proliferation by affecting ribosome biogenesis or by another nucleolus-based activity that is specific to stem cells and/or highly proliferating cells. Here, we investigate nucleostemin (nst-1) in the nematode C. elegans, which enables us to examine nst-1 function during both proliferation and differentiation in vivo. Like mammalian nucleostemin, the NST-1 protein is localized to the nucleolus and the nucleoplasm; however, its expression is found in both differentiated and proliferating cells. Global loss of C. elegans nucleostemin (nst-1) leads to a larval arrest phenotype due to a growth defect in the soma, while loss of nst-1 specifically in the germ line causes germline stem cells to undergo a cell cycle arrest. nst-1 mutants exhibit reduced levels of rRNAs, suggesting defects in ribosome biogenesis. However, NST-1 is generally not present in regions of the nucleolus where rRNA transcription and processing occurs, so this reduction is likely secondary to a different defect in ribosome biogenesis. Transgenic studies indicate that NST-1 requires its N-terminal domain for stable expression and both its G1 GTPase and intermediate domains for proper germ line function. Our data support a role for C. elegans nucleostemin in cell growth and proliferation by promoting ribosome biogenesis. Stem cells are carefully poised between the alternate fates of proliferation and differentiation. The regulation of this choice is a complex one that occurs on many different levels. One major influence controlling this choice derives signals emanating from the nucleolus, which serves dual roles as the site of ribosome biogenesis and as a repository for sequestered key regulatory factors. The nucleolar GTPase nucleostemin has recently been identified as a potential link between stem cell proliferation and nucleolar function, but its exact role in the nucleolus has not been directly addressed in a metazoan. Here, we use the model organism C. elegans to investigate the function of nucleostemin in both differentiated cells and proliferating stem cells. We show that nucleostemin probably acts to regulate ribosome biogenesis, and through this process controls cell proliferation. We also suggest that, at least in C. elegans, the function of nucleostemin is not restricted to proliferating stem cells, but that it also functions in differentiated cells to control cell growth. Our study highlights the complexity of the role of the nucleolus in regulation of cell growth and division.
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Hyenne V, Desrosiers M, Labbé JC. C. elegans Brat homologs regulate PAR protein-dependent polarity and asymmetric cell division. Dev Biol 2008; 321:368-78. [PMID: 18652816 DOI: 10.1016/j.ydbio.2008.06.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Revised: 06/25/2008] [Accepted: 06/25/2008] [Indexed: 12/18/2022]
Abstract
The evolutionary conserved PAR proteins control polarization and asymmetric division in many organisms. Recent work in Caenorhabditis elegans demonstrated that nos-3 and fbf-1/2 can suppress par-2(it5ts) lethality, suggesting that they participate in cell polarity by regulating the function of the anterior PAR-3/PAR-6/PKC-3 proteins. In Drosophila embryos, Nanos and Pumilio are homologous to NOS-3 and FBF-1/2 respectively and control cell polarity by forming a complex with the tumor suppressor Brat to inhibit Hunchback mRNA translation. In this study, we investigated the possibility that Brat could control cell polarity and asymmetric cell division in C. elegans. We found that disrupting four of the five C. elegans Brat homologs (Cebrats) individually results in suppression of par-2(it5ts) lethality, indicating that these genes are involved in embryonic polarity. Two of the Cebrats, ncl-1 and nhl-2, partially restore the localization of PAR proteins at the cortex. While mutations in the four Cebrat genes do not severely impair polarity, they display polarity-associated defects. Surprisingly, these defects are absent from nos-3 mutants. Similarly, while nos-3 controls PAR-6 protein levels, this is not the case for any of the Cebrats. Our results, together with results from Drosophila, indicate that Brat family members function in generating cellular asymmetries and suggest that, in contrast to Drosophila embryos, the C. elegans homologs of Brat and Nanos could participate in embryonic polarity via distinct mechanisms.
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Affiliation(s)
- Vincent Hyenne
- Cell Division and Differentiation Laboratory, Institute of Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succ Centre-ville Montréal, QC Canada H3C 3J7.
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Kiefer JC, Smith PA, Mango SE. PHA-4/FoxA cooperates with TAM-1/TRIM to regulate cell fate restriction in the C. elegans foregut. Dev Biol 2006; 303:611-24. [PMID: 17250823 PMCID: PMC1855296 DOI: 10.1016/j.ydbio.2006.11.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 11/16/2006] [Accepted: 11/28/2006] [Indexed: 10/23/2022]
Abstract
A key question in development is how pluripotent progenitors are progressively restricted to acquire specific cell fates. Here we investigate how embryonic blastomeres in C. elegans develop into foregut (pharynx) cells in response to the selector gene PHA-4/FoxA. When pha-4 is removed from pharyngeal precursors, they exhibit two alternative responses. Before late-gastrulation (8E stage), these cells lose their pharyngeal identity and acquire an alternative fate such as ectoderm (Specification stage). After the Specification stage, mutant cells develop into aberrant pharyngeal cells (Morphogenesis/Differentiation stage). Two lines of evidence suggest that the Specification stage depends on transcriptional repression of ectodermal genes by pha-4. First, pha-4 exhibits strong synthetic phenotypes with the B class synMuv gene tam-1 (Tandam Array expression Modifier 1) and with a mediator of transcriptional repression, the NuRD complex (NUcleosome Remodeling and histone Deacetylase). Second, pha-4 associates with the promoter of the ectodermal regulator lin-26 and is required to repress lin-26 expression. We propose that restriction of early blastomeres to the pharyngeal fate depends on both repression of ectodermal genes and activation of pharyngeal genes by PHA-4.
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Affiliation(s)
| | | | - Susan E. Mango
- *To whom correspondence should be sent: , phone 801-581-7633, FAX 801-585- 1980
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Abstract
The nucleolus is the most prominent compartment in the nucleus and known as the site for ribosome biogenesis in eucaryotes. In contrast, there is no such equivalent structure for ribosome synthesis in procaryotes. This raises two concerns that how does the nucleolus evolve and that whether the nucleolus remains playing a single role in ribosome biogenesis along the evolution. Increasing data support new nucleolus functions, including signal recognition particle assembly, small RNA modification, telomerase maturation, cell-cycle and aging control, and cell stress sensor. Multiple functions of the nucleolus possibly result from the plurifunctionality of nucleolar proteins, such as nucleolin and Nopp140. Proteomic analyses of human and Arabidopsis nucleolus lead a remarkable progress in understanding the evolution and new functions of nucleoli. In this review, we present a brief history of nucleolus research and new concepts and unresolved questions. Also, we introduce hepatitis D virus for studying the communication between the nucleolus and other subnuclear compartments, and Caenorhabditis elegans for the role of nucleolus in the development and the epistatic control of nucleologenesis.
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Affiliation(s)
- Szecheng J Lo
- Department of Life Science, Graduate Institute of Basic Medical Science, 259, Wen-Hwa 1st Road, Chang Gung University, TaoYuan 333.
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Meroni G, Diez-Roux G. TRIM/RBCC, a novel class of 'single protein RING finger' E3 ubiquitin ligases. Bioessays 2006; 27:1147-57. [PMID: 16237670 DOI: 10.1002/bies.20304] [Citation(s) in RCA: 529] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The TRIM/RBCC proteins are defined by the presence of the tripartite motif composed of a RING domain, one or two B-box motifs and a coiled-coil region. These proteins are involved in a plethora of cellular processes such as apoptosis, cell cycle regulation and viral response. Consistently, their alteration results in many diverse pathological conditions. The highly conserved modular structure of these proteins suggests that a common biochemical function may underlie their assorted cellular roles. Here, we review recent data indicating that some TRIM/RBCC proteins are implicated in ubiquitination and propose that this large protein family represents a novel class of 'single protein RING finger' ubiquitin E3 ligases.
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Affiliation(s)
- Germana Meroni
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy.
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Voutev R, Killian DJ, Ahn JH, Hubbard EJA. Alterations in ribosome biogenesis cause specific defects in C. elegans hermaphrodite gonadogenesis. Dev Biol 2006; 298:45-58. [PMID: 16876152 DOI: 10.1016/j.ydbio.2006.06.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2006] [Revised: 05/21/2006] [Accepted: 06/02/2006] [Indexed: 12/16/2022]
Abstract
Ribosome biogenesis is a cell-essential process that influences cell growth, proliferation, and differentiation. How ribosome biogenesis impacts development, however, is poorly understood. Here, we establish a link between ribosome biogenesis and gonadogenesis in Caenorhabditis elegans that affects germline proliferation and patterning. Previously, we determined that pro-1(+)activity is required in the soma--specifically, the sheath/spermatheca sublineage--to promote normal proliferation and prevent germline tumor formation. Here, we report that PRO-1, like its yeast ortholog IPI3, influences rRNA processing. pro-1 tumors are suppressed by mutations in ncl-1 or lin-35/Rb, both of which elevate pre-rRNA levels. Thus, in this context, lin-35/Rb acts as a soma-autonomous germline tumor promoter. We further report the characterization of two additional genes identified for their germline tumor phenotype, pro-2 and pro-3, and find that they, too, encode orthologs of proteins involved in ribosome biogenesis in yeast (NOC2 and SDA1, respectively). Finally, we demonstrate that depletion of additional C. elegans orthologs of yeast ribosome biogenesis factors display phenotypes similar to depletion of progenes. We conclude that the C. elegans distal sheath is particularly sensitive to alterations in ribosome biogenesis and that ribosome biogenesis defects in one tissue can non-autonomously influence proliferation in an adjacent tissue.
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Affiliation(s)
- Roumen Voutev
- Department of Biology, New York University, New York, NY 10003-6688, USA
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Gonzalez-Serricchio AS, Sternberg PW. Visualization of C. elegans transgenic arrays by GFP. BMC Genet 2006; 7:36. [PMID: 16759392 PMCID: PMC1539001 DOI: 10.1186/1471-2156-7-36] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Accepted: 06/07/2006] [Indexed: 11/15/2022] Open
Abstract
Background Targeting the green fluorescent protein (GFP) via the E. coli lac repressor (LacI) to a specific DNA sequence, the lac operator (lacO), allows visualization of chromosomes in yeast and mammalian cells. In principle this method of visualization could be used for genetic mosaic analysis, which requires cell-autonomous markers that can be scored easily and at single cell resolution. The C. elegans lin-3 gene encodes an epidermal growth factor family (EGF) growth factor. lin-3 is expressed in the gonadal anchor cell and acts through LET-23 (transmembrane protein tyrosine kinase and ortholog of EGF receptor) to signal the vulval precursor cells to generate vulval tissue. lin-3 is expressed in the vulval cells later, and recent evidence raises the possibility that lin-3 acts in the vulval cells as a relay signal during vulval induction. It is thus of interest to test the site of action of lin-3 by mosaic analysis. Results We visualized transgenes in living C. elegans by targeting the green fluorescent protein (GFP) via the E. coli lac repressor (LacI) to a specific 256 sequence repeat of the lac operator (lacO) incorporated into transgenes. We engineered animals to express a nuclear-localized GFP-LacI fusion protein. C. elegans cells having a lacO transgene result in nuclear-localized bright spots (i.e., GFP-LacI bound to lacO). Cells with diffuse nuclear fluorescence correspond to unbound nuclear localized GFP-LacI. We detected chromosomes in living animals by chromosomally integrating the array of the lacO repeat sequence and visualizing the integrated transgene with GFP-LacI. This detection system can be applied to determine polyploidy as well as investigating chromosome segregation. To assess the GFP-LacI•lacO system as a marker for mosaic analysis, we conducted genetic mosaic analysis of the epidermal growth factor lin-3, expressed in the anchor cell. We establish that lin-3 acts in the anchor cell to induce vulva development, demonstrating this method's utility in detecting the presence of a transgene. Conclusion The GFP-LacI•lacO transgene detection system works in C. elegans for visualization of chromosomes and extrachromosomal transgenes. It can be used as a marker for genetic mosaic analysis. The lacO repeat sequence as an extrachromosomal array becomes a valuable technique allowing rapid, accurate determination of spontaneous loss of the array, thereby allowing high-resolution mosaic analysis. The lin-3 gene is required in the anchor cell to induce the epidermal vulval precursors cells to undergo vulval development.
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Affiliation(s)
- Aidyl S Gonzalez-Serricchio
- Department of Biological Sciences, California State Polytechnic University, 3801 W Temple Avenue, Pomona, CA 91768, USA
| | - Paul W Sternberg
- Division of Biology and Howard Hughes Medical Institute, mail code 156-29, Caltech, Pasadena, CA 91125, USA
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Betschinger J, Mechtler K, Knoblich JA. Asymmetric segregation of the tumor suppressor brat regulates self-renewal in Drosophila neural stem cells. Cell 2006; 124:1241-53. [PMID: 16564014 DOI: 10.1016/j.cell.2006.01.038] [Citation(s) in RCA: 396] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Revised: 12/01/2005] [Accepted: 01/03/2006] [Indexed: 12/22/2022]
Abstract
How stem cells generate both differentiating and self-renewing daughter cells is unclear. Here, we show that Drosophila larval neuroblasts-stem cell-like precursors of the adult brain-regulate proliferation by segregating the growth inhibitor Brat and the transcription factor Prospero into only one daughter cell. Like Prospero, Brat binds and cosegregates with the adaptor protein Miranda. In larval neuroblasts, both Brat and Prospero are required to inhibit self-renewal in one of the two daughter cells. While Prospero regulates cell-cycle gene transcription, Brat acts as a posttranscriptional inhibitor of dMyc. In brat or prospero mutants, both daughter cells grow and behave like neuroblasts leading to the formation of larval brain tumors. Similar defects are seen in lethal giant larvae (lgl) mutants where Brat and Prospero are not asymmetric. We have identified a molecular mechanism that may control self-renewal and prevent tumor formation in other stem cells as well.
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Affiliation(s)
- Joerg Betschinger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr Bohr Gasse 3-5, 1030 Vienna, Austria
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Bates EA, Victor M, Jones AK, Shi Y, Hart AC. Differential contributions of Caenorhabditis elegans histone deacetylases to huntingtin polyglutamine toxicity. J Neurosci 2006; 26:2830-8. [PMID: 16525063 PMCID: PMC6675170 DOI: 10.1523/jneurosci.3344-05.2006] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Expansion of a polyglutamine tract in the huntingtin protein causes neuronal degeneration and death in Huntington's disease patients, but the molecular mechanisms underlying polyglutamine-mediated cell death remain unclear. Previous studies suggest that expanded polyglutamine tracts alter transcription by sequestering glutamine rich transcriptional regulatory proteins, thereby perturbing their function. We tested this hypothesis in Caenorhabditis elegans neurons expressing a human huntingtin fragment with an expanded polyglutamine tract (Htn-Q150). Loss of function alleles and RNA interference (RNAi) were used to examine contributions of C. elegans cAMP response element-binding protein (CREB), CREB binding protein (CBP), and histone deacetylases (HDACs) to polyglutamine-induced neurodegeneration. Deletion of CREB (crh-1) or loss of one copy of CBP (cbp-1) enhanced polyglutamine toxicity in C. elegans neurons. Loss of function alleles and RNAi were then used to systematically reduce function of each C. elegans HDAC. Generally, knockdown of individual C. elegans HDACs enhanced Htn-Q150 toxicity, but knockdown of C. elegans hda-3 suppressed toxicity. Neuronal expression of hda-3 restored Htn-Q150 toxicity and suggested that C. elegans HDAC3 (HDA-3) acts within neurons to promote degeneration in response to Htn-Q150. Genetic epistasis experiments suggested that HDA-3 and CRH-1 (C. elegans CREB homolog) directly oppose each other in regulating transcription of genes involved in polyglutamine toxicity. hda-3 loss of function failed to suppress increased neurodegeneration in hda-1/+;Htn-Q150 animals, indicating that HDA-1 and HDA-3 have different targets with opposing effects on polyglutamine toxicity. Our results suggest that polyglutamine expansions perturb transcription of CREB/CBP targets and that specific targeting of HDACs will be useful in reducing associated neurodegeneration.
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van Diepen MT, Spencer GE, van Minnen J, Gouwenberg Y, Bouwman J, Smit AB, van Kesteren RE. The molluscan RING-finger protein L-TRIM is essential for neuronal outgrowth. Mol Cell Neurosci 2005; 29:74-81. [PMID: 15866048 DOI: 10.1016/j.mcn.2005.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2004] [Accepted: 01/17/2005] [Indexed: 01/23/2023] Open
Abstract
The tripartite motif proteins TRIM-2 and TRIM-3 have been put forward as putative organizers of neuronal outgrowth and structural plasticity. Here, we identified a molluscan orthologue of TRIM-2/3, named L-TRIM, which is up-regulated during in vitro neurite outgrowth of central neurons. In adult animals, L-Trim mRNA is ubiquitously expressed at low levels in the central nervous system and in peripheral tissues. Central nervous system expression of L-Trim mRNA is increased during postnatal brain development and during in vitro and in vivo neuronal regeneration. In vitro double-stranded RNA knock-down of L-Trim mRNA resulted in a >70% inhibition of neurite outgrowth. Together, our data establish a crucial role for L-TRIM in developmental neurite outgrowth and functional neuronal regeneration and indicate that TRIM-2/3 family members may have evolutionary conserved functions in neuronal differentiation.
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Affiliation(s)
- M T van Diepen
- Department of Molecular and Cellular Neurobiology, Faculty of Earth and Life Sciences, Institute of Neuroscience, Vrije Universiteit, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
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Glasscock E, Singhania A, Tanouye MA. The mei-P26 gene encodes a RING finger B-box coiled-coil-NHL protein that regulates seizure susceptibility in Drosophilia. Genetics 2005; 170:1677-89. [PMID: 15937125 PMCID: PMC1449765 DOI: 10.1534/genetics.105.043174] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seizure-suppressor mutations provide unique insight into the genes and mechanisms involved in regulating nervous system excitability. Drosophila bang-sensitive (BS) mutants present a useful tool for identifying seizure suppressors since they are a well-characterized epilepsy model. Here we describe the isolation and characterization of a new Drosophila seizure-suppressor mutant that results from disruption of the meiotic gene mei-P26, which belongs to the RBCC-NHL family of proteins. The mei-P26 mutation reduces seizures in easily shocked (eas) and slamdance (sda) epileptic flies following mechanical stimulation and electroconvulsive shock. In addition, mutant mei-P26 flies exhibit seizure thresholds at least threefold greater than those of wild type. The mei-P26 phenotypes appear to result from missense mutation of a critical residue in the NHL protein-protein interaction domain of the protein. These results reveal a surprising role for mei-P26 outside of the germline as a regulator of seizure susceptibility, possibly by affecting synaptic development as a ubiquitin ligase.
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Affiliation(s)
- Edward Glasscock
- Department of Molecular and Cell Biology, Division of Neurobiology, University of California, Berkeley, CA 94720, USA.
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50
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Abstract
Size is a fundamental attribute impacting cellular design, fitness, and function. Size homeostasis requires a doubling of cell mass with each division. In yeast, division is delayed until a critical size has been achieved. In metazoans, cell cycles can be actively coupled to growth, but in certain cell types extracellular signals may independently induce growth and division. Despite a long history of study, the fascinating mechanisms that control cell size have resisted molecular genetic insight. Recently, genetic screens in Drosophila and functional genomics approaches in yeast have macheted into the thicket of cell size control.
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Affiliation(s)
- Paul Jorgensen
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON, Canada M5S 1A8.
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