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Wahiduzzaman, Tindell SJ, Alexander E, Hackney E, Kharel K, Schmidtke R, Arkov AL. Drosophila germ granules are assembled from protein components through different modes of competing interactions with the multi-domain Tudor protein. FEBS Lett 2024; 598:774-786. [PMID: 38499396 DOI: 10.1002/1873-3468.14846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/21/2023] [Accepted: 02/14/2024] [Indexed: 03/20/2024]
Abstract
Membraneless organelles are RNA-protein assemblies which have been implicated in post-transcriptional control. Germ cells form membraneless organelles referred to as germ granules, which contain conserved proteins including Tudor domain-containing scaffold polypeptides and their partner proteins that interact with Tudor domains. Here, we show that in Drosophila, different germ granule proteins associate with the multi-domain Tudor protein using different numbers of Tudor domains. Furthermore, these proteins compete for interaction with Tudor in vitro and, surprisingly, partition to distinct and poorly overlapping clusters in germ granules in vivo. This partition results in minimization of the competition. Our data suggest that Tudor forms structurally different configurations with different partner proteins which dictate different biophysical properties and phase separation parameters within the same granule.
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Affiliation(s)
- Wahiduzzaman
- Department of Biological Sciences, Murray State University, KY, USA
| | - Samuel J Tindell
- Department of Biological Sciences, Murray State University, KY, USA
| | - Emma Alexander
- Department of Biological Sciences, Murray State University, KY, USA
| | - Ethan Hackney
- Department of Biological Sciences, Murray State University, KY, USA
| | - Kabita Kharel
- Department of Biological Sciences, Murray State University, KY, USA
| | - Ryan Schmidtke
- Department of Biological Sciences, Murray State University, KY, USA
| | - Alexey L Arkov
- Department of Biological Sciences, Murray State University, KY, USA
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2
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Arkov AL. Looking at the Pretty "Phase" of Membraneless Organelles: A View From Drosophila Glia. Front Cell Dev Biol 2022; 10:801953. [PMID: 35198559 PMCID: PMC8859445 DOI: 10.3389/fcell.2022.801953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Membraneless granules assemble in different cell types and cellular loci and are the focus of intense research due to their fundamental importance for cellular organization. These dynamic organelles are commonly assembled from RNA and protein components and exhibit soft matter characteristics of molecular condensates currently characterized with biophysical approaches and super-resolution microscopy imaging. In addition, research on the molecular mechanisms of the RNA-protein granules assembly provided insights into the formation of abnormal granules and molecular aggregates, which takes place during many neurodegenerative disorders including Parkinson's diseases (PD), Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). While these disorders are associated with formation of abnormal granules, membraneless organelles are normally assembled in neurons and contribute to translational control and affect stability of neuronal RNAs. More recently, a new subtype of membraneless granules was identified in Drosophila glia (glial granules). Interestingly, glial granules were found to contain proteins which are the principal components of the membraneless granules in germ cells (germ granules), indicating some similarity in the functional assembly of these structures in glia and germline. This mini review highlights recent research on glial granules in the context of other membraneless organelles, including their assembly mechanisms and potential functions in the nervous system.
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Affiliation(s)
- Alexey L Arkov
- Department of Biological Sciences, Murray State University, Murray, KY, United States
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3
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Tindell SJ, Rouchka EC, Arkov AL. Glial granules contain germline proteins in the Drosophila brain, which regulate brain transcriptome. Commun Biol 2020; 3:699. [PMID: 33219296 PMCID: PMC7679405 DOI: 10.1038/s42003-020-01432-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/23/2020] [Indexed: 01/23/2023] Open
Abstract
Membraneless RNA-protein granules play important roles in many different cell types and organisms. In particular, granules found in germ cells have been used as a paradigm to study large and dynamic granules. These germ granules contain RNA and proteins required for germline development. Here, we unexpectedly identify large granules in specific subtypes of glial cells ("glial granules") of the adult Drosophila brain which contain polypeptides with previously characterized roles in germ cells including scaffold Tudor, Vasa, Polar granule component and Piwi family proteins. Interestingly, our super-resolution microscopy analysis shows that in the glial granules, these proteins form distinct partially overlapping clusters. Furthermore, we show that glial granule scaffold protein Tudor functions in silencing of transposable elements and in small regulatory piRNA biogenesis. Remarkably, our data indicate that the adult brain contains a small population of cells, which express both neuroblast and germ cell proteins. These distinct cells are evolutionarily conserved and expand during aging suggesting the existence of age-dependent signaling. Our work uncovers previously unknown glial granules and indicates the involvement of their components in the regulation of brain transcriptome.
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Affiliation(s)
- Samuel J Tindell
- Department of Biological Sciences, Murray State University, Murray, KY, 42071, USA
| | - Eric C Rouchka
- Computer Science and Engineering Department, University of Louisville, Louisville, KY, 40292, USA
| | - Alexey L Arkov
- Department of Biological Sciences, Murray State University, Murray, KY, 42071, USA.
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4
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Abstract
RNA granules are ubiquitous. Composed of RNA-binding proteins and RNAs, they provide functional compartmentalization within cells. They are inextricably linked with RNA biology and as such are often referred to as the hubs for post-transcriptional regulation. Much of the attention has been given to the proteins that form these condensates and thus many fundamental questions about the biology of RNA granules remain poorly understood: How and which RNAs enrich in RNA granules, how are transcripts regulated in them, and how do granule-enriched mRNAs shape the biology of a cell? In this review, we discuss the imaging, genetic, and biochemical data, which have revealed that some aspects of the RNA biology within granules are carried out by the RNA itself rather than the granule proteins. Interestingly, the RNA structure has emerged as an important feature in the post-transcriptional control of granule transcripts. This review is part of the Special Issue in the Frontiers in RNA structure in the journal Molecules.
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Affiliation(s)
| | | | - Tatjana Trcek
- Homewood Campus, Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA; (S.T.); (H.A.C.)
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5
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Trcek T, Douglas TE, Grosch M, Yin Y, Eagle WVI, Gavis ER, Shroff H, Rothenberg E, Lehmann R. Sequence-Independent Self-Assembly of Germ Granule mRNAs into Homotypic Clusters. Mol Cell 2020; 78:941-950.e12. [PMID: 32464092 DOI: 10.1016/j.molcel.2020.05.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/29/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022]
Abstract
mRNAs enriched in membraneless condensates provide functional compartmentalization within cells. The mechanisms that recruit transcripts to condensates are under intense study; however, how mRNAs organize once they reach a granule remains poorly understood. Here, we report on a self-sorting mechanism by which multiple mRNAs derived from the same gene assemble into discrete homotypic clusters. We demonstrate that in vivo mRNA localization to granules and self-assembly within granules are governed by different mRNA features: localization is encoded by specific RNA regions, whereas self-assembly involves the entire mRNA, does not involve sequence-specific, ordered intermolecular RNA:RNA interactions, and is thus RNA sequence independent. We propose that the ability of mRNAs to self-sort into homotypic assemblies is an inherent property of an messenger ribonucleoprotein (mRNP) that is augmented under conditions that increase RNA concentration, such as upon enrichment in RNA-protein granules, a process that appears conserved in diverse cellular contexts and organisms.
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Affiliation(s)
- Tatjana Trcek
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA.
| | - Tyler E Douglas
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA
| | - Markus Grosch
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA
| | - Yandong Yin
- Department of Biochemistry and Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Whitby V I Eagle
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Elizabeth R Gavis
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD, USA
| | - Eli Rothenberg
- Department of Biochemistry and Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Ruth Lehmann
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA.
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Vo HDL, Wahiduzzaman, Tindell SJ, Zheng J, Gao M, Arkov AL. Protein components of ribonucleoprotein granules from Drosophila germ cells oligomerize and show distinct spatial organization during germline development. Sci Rep 2019; 9:19190. [PMID: 31844131 PMCID: PMC6915754 DOI: 10.1038/s41598-019-55747-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/28/2019] [Indexed: 01/11/2023] Open
Abstract
The assembly of large RNA-protein granules occurs in germ cells of many animals and these germ granules have provided a paradigm to study structure-functional aspects of similar structures in different cells. Germ granules in Drosophila oocyte’s posterior pole (polar granules) are composed of RNA, in the form of homotypic clusters, and proteins required for germline development. In the granules, Piwi protein Aubergine binds to a scaffold protein Tudor, which contains 11 Tudor domains. Using a super-resolution microscopy, we show that surprisingly, Aubergine and Tudor form distinct clusters within the same polar granules in early Drosophila embryos. These clusters partially overlap and, after germ cells form, they transition into spherical granules with the structural organization unexpected from these interacting proteins: Aubergine shell around the Tudor core. Consistent with the formation of distinct clusters, we show that Aubergine forms homo-oligomers and using all purified Tudor domains, we demonstrate that multiple domains, distributed along the entire Tudor structure, interact with Aubergine. Our data suggest that in polar granules, Aubergine and Tudor are assembled into distinct phases, partially mixed at their “interaction hubs”, and that association of distinct protein clusters may be an evolutionarily conserved mechanism for the assembly of germ granules.
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Affiliation(s)
- Hieu D L Vo
- Department of Biological Sciences, Murray State University, Murray, KY, 42071, USA
| | - Wahiduzzaman
- Department of Biological Sciences, Murray State University, Murray, KY, 42071, USA
| | - Samuel J Tindell
- Department of Biological Sciences, Murray State University, Murray, KY, 42071, USA
| | - Jimiao Zheng
- Department of Biological Sciences, Murray State University, Murray, KY, 42071, USA
| | - Ming Gao
- Biology Department, Indiana University Northwest, Gary, IN, 46408, USA
| | - Alexey L Arkov
- Department of Biological Sciences, Murray State University, Murray, KY, 42071, USA.
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Miura S, Kosaka K, Nomura T, Nagata S, Shimojo T, Morikawa T, Fujioka R, Harada M, Taniwaki T, Shibata H. TDRKH is a candidate gene for an autosomal dominant distal hereditary motor neuropathy. Eur J Med Genet 2019; 62:103594. [DOI: 10.1016/j.ejmg.2018.11.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 01/06/2023]
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Kistler KE, Trcek T, Hurd TR, Chen R, Liang FX, Sall J, Kato M, Lehmann R. Phase transitioned nuclear Oskar promotes cell division of Drosophila primordial germ cells. eLife 2018; 7:37949. [PMID: 30260314 PMCID: PMC6191285 DOI: 10.7554/elife.37949] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/09/2018] [Indexed: 12/25/2022] Open
Abstract
Germ granules are non-membranous ribonucleoprotein granules deemed the hubs for post-transcriptional gene regulation and functionally linked to germ cell fate across species. Little is known about the physical properties of germ granules and how these relate to germ cell function. Here we study two types of germ granules in the Drosophila embryo: cytoplasmic germ granules that instruct primordial germ cells (PGCs) formation and nuclear germ granules within early PGCs with unknown function. We show that cytoplasmic and nuclear germ granules are phase transitioned condensates nucleated by Oskar protein that display liquid as well as hydrogel-like properties. Focusing on nuclear granules, we find that Oskar drives their formation in heterologous cell systems. Multiple, independent Oskar protein domains synergize to promote granule phase separation. Deletion of Oskar’s nuclear localization sequence specifically ablates nuclear granules in cell systems. In the embryo, nuclear germ granules promote germ cell divisions thereby increasing PGC number for the next generation.
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Affiliation(s)
- Kathryn E Kistler
- Skirball Institute of Biomolecular Medicine, Howard Hughes Medical Institute, NYU School of Medicine, New York, United States.,Department of Molecular and Cellular Biology, University of Washington, Washington, United States
| | - Tatjana Trcek
- Skirball Institute of Biomolecular Medicine, Howard Hughes Medical Institute, NYU School of Medicine, New York, United States
| | - Thomas R Hurd
- Skirball Institute of Biomolecular Medicine, Howard Hughes Medical Institute, NYU School of Medicine, New York, United States.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Ruoyu Chen
- Skirball Institute of Biomolecular Medicine, Howard Hughes Medical Institute, NYU School of Medicine, New York, United States
| | - Feng-Xia Liang
- Department of Cell Biology, NYU School of Medicine, New York, United States.,DART Microscopy Laboratory, NYU Langone Health, New York, United States
| | - Joseph Sall
- DART Microscopy Laboratory, NYU Langone Health, New York, United States
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Texas, United States
| | - Ruth Lehmann
- Skirball Institute of Biomolecular Medicine, Howard Hughes Medical Institute, NYU School of Medicine, New York, United States.,Department of Cell Biology, NYU School of Medicine, New York, United States
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9
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Abstract
PIWI proteins and Piwi-interacting RNAs (piRNAs) have established and conserved roles in repressing transposable elements (TEs) in the germline of animals. However, in several biological contexts, a large proportion of piRNAs are not related to TE sequences and, accordingly, functions for piRNAs and PIWI proteins that are independent of TE regulation have been identified. This aspect of piRNA biology is expanding rapidly. Indeed, recent reports have revealed the role of piRNAs in the regulation of endogenous gene expression programs in germ cells, as well as in somatic tissues, challenging dogma in the piRNA field. In this Review, we focus on recent data addressing the biological and developmental functions of piRNAs, highlighting their roles in embryonic patterning, germ cell specification, stem cell biology, neuronal activity and metabolism.
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Affiliation(s)
- Patricia Rojas-Ríos
- mRNA Regulation and Development, IGH, Univ. Montpellier, CNRS, Montpellier 34396, France
| | - Martine Simonelig
- mRNA Regulation and Development, IGH, Univ. Montpellier, CNRS, Montpellier 34396, France
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10
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Abstract
Gene regulation by PIWI-piRNA complexes is determined by the selection of cognate target RNAs by PIWI-piRNA. What are the mechanisms for this selection? There is a rigorous multistep control in identifying target RNAs by PIWI-piRNA structures, and RNA helicases play a potentially crucial role in this process.
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Affiliation(s)
- Alexey L Arkov
- Department of Biological Sciences, Murray State University, Murray, KY 42071, USA.
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11
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DeHaan H, McCambridge A, Armstrong B, Cruse C, Solanki D, Trinidad JC, Arkov AL, Gao M. An in vivo proteomic analysis of the Me31B interactome in Drosophila germ granules. FEBS Lett 2017; 591:3536-3547. [PMID: 28945271 DOI: 10.1002/1873-3468.12854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/07/2017] [Accepted: 09/15/2017] [Indexed: 12/11/2022]
Abstract
Drosophila Me31B is a conserved protein of germ granules, ribonucleoprotein complexes essential for germ cell development. Me31B post-transcriptionally regulates mRNAs by interacting with other germ granule proteins. However, a Me31B interactome is lacking. Here, we use an in vivo proteomics approach to show that the Me31B interactome contains polypeptides from four functional groups: RNA regulatory proteins, glycolytic enzymes, cytoskeleton/motor proteins, and germ plasm components. We further show that Me31B likely colocalizes with the germ plasm components Tudor (Tud), Vasa, and Aubergine in the nuage and germ plasm and provide evidence that Me31B may directly bind to Tud in a symmetrically dimethylated arginine-dependent manner. Our study supports the role of Me31B in RNA regulation and suggests its novel roles in germ granule assembly and function.
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Affiliation(s)
- Hunter DeHaan
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | | | | | - Carlie Cruse
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Dhruv Solanki
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | | | - Alexey L Arkov
- Department of Biological Sciences, Murray State University, Murray, KY, USA
| | - Ming Gao
- Biology Department, Indiana University Northwest, Gary, IN, USA
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