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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] [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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Marnik EA, Almeida MV, Cipriani PG, Chung G, Caspani E, Karaulanov E, Gan HH, Zinno J, Isolehto IJ, Kielisch F, Butter F, Sharp CS, Flanagan RM, Bonnet FX, Piano F, Ketting RF, Gunsalus KC, Updike DL. The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline. PLoS Genet 2022; 18:e1010245. [PMID: 35657999 PMCID: PMC9200344 DOI: 10.1371/journal.pgen.1010245] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 06/15/2022] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
LOTUS and Tudor domain containing proteins have critical roles in the germline. Proteins that contain these domains, such as Tejas/Tapas in Drosophila, help localize the Vasa helicase to the germ granules and facilitate piRNA-mediated transposon silencing. The homologous proteins in mammals, TDRD5 and TDRD7, are required during spermiogenesis. Until now, proteins containing both LOTUS and Tudor domains in Caenorhabditis elegans have remained elusive. Here we describe LOTR-1 (D1081.7), which derives its name from its LOTUS and Tudor domains. Interestingly, LOTR-1 docks next to P granules to colocalize with the broadly conserved Z-granule helicase, ZNFX-1. The Tudor domain of LOTR-1 is required for its Z-granule retention. Like znfx-1 mutants, lotr-1 mutants lose small RNAs from the 3’ ends of WAGO and mutator targets, reminiscent of the loss of piRNAs from the 3’ ends of piRNA precursor transcripts in mouse Tdrd5 mutants. Our work shows that LOTR-1 acts with ZNFX-1 to bring small RNA amplifying mechanisms towards the 3’ ends of its RNA templates. Germ granules are protein and RNA complexes that are critical for maintaining an animal’s fertility. Central to the composition of germ granules are their small RNAs, which have the capacity to convey a memory of germline-licensed expression from one generation to the next. Here we describe and characterize a new germ-granule protein in C. elegans that we’ve named LOTR-1, after its LOTUS and Tudor domains. This combination of LOTUS and Tudor domains can be found in the mammalian proteins TDRD5 and TDRD7, which are required during spermatogenesis. During C. elegans embryogenesis, germ granules demix or partition into subgranules with refined functions. We show that LOTR-1 partitions with a specific class of subgranules called Z granules, interacting with a Z-granule helicase called ZNFX-1. Here, LOTR-1 functions with ZNFX-1 to position small RNA amplification from RNA templates, ensuring a memory of germline expression across generations. These findings may provide new insight into the function of TDRD5 and TDRD7 during human germline development.
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Affiliation(s)
- Elisabeth A. Marnik
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
- Husson University, Bangor, Maine, United States of America
| | - Miguel V. Almeida
- Institute of Molecular Biology, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | - P. Giselle Cipriani
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - George Chung
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Edoardo Caspani
- Institute of Molecular Biology, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | | | - Hin Hark Gan
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - John Zinno
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Ida J. Isolehto
- Institute of Molecular Biology, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | | | - Falk Butter
- Institute of Molecular Biology, Mainz, Germany
| | - Catherine S. Sharp
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Roisin M. Flanagan
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Frederic X. Bonnet
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Fabio Piano
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - René F. Ketting
- Institute of Molecular Biology, Mainz, Germany
- * E-mail: (RFK); (KCG); (DLU)
| | - Kristin C. Gunsalus
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- * E-mail: (RFK); (KCG); (DLU)
| | - Dustin L. Updike
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
- * E-mail: (RFK); (KCG); (DLU)
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Kemph A, Lynch JA. Evolution of germ plasm assembly and function among the insects. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100883. [PMID: 35123121 PMCID: PMC9133133 DOI: 10.1016/j.cois.2022.100883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/13/2022] [Accepted: 01/24/2022] [Indexed: 05/04/2023]
Abstract
Germ plasm is a substance capable of driving naive cells toward the germ cell fate. Germ plasm has had multiple independent origins, and takes on diverse forms and functions throughout animals, including in insects. We describe here recent advances in the understanding of the evolution of germ plasm in insects. A major theme that has emerged is the complex and convoluted interactions of germ plasm with symbiotic bacteria within the germline, including at the very origin of oskar, the gene required for assembling germ plasm in insects. Major advancements have also been made in understanding the basic molecular arrangement of germ plasm in insects. These advances demonstrate that further analysis of insect germ plasm will be fruitful in illuminating diverse aspects of evolutionary and developmental biology.
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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] [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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van Alphen B, Stewart S, Iwanaszko M, Xu F, Li K, Rozenfeld S, Ramakrishnan A, Itoh TQ, Sisobhan S, Qin Z, Lear BC, Allada R. Glial immune-related pathways mediate effects of closed head traumatic brain injury on behavior and lethality in Drosophila. PLoS Biol 2022; 20:e3001456. [PMID: 35081110 PMCID: PMC8791498 DOI: 10.1371/journal.pbio.3001456] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/22/2021] [Indexed: 02/07/2023] Open
Abstract
In traumatic brain injury (TBI), the initial injury phase is followed by a secondary phase that contributes to neurodegeneration, yet the mechanisms leading to neuropathology in vivo remain to be elucidated. To address this question, we developed a Drosophila head-specific model for TBI termed Drosophila Closed Head Injury (dCHI), where well-controlled, nonpenetrating strikes are delivered to the head of unanesthetized flies. This assay recapitulates many TBI phenotypes, including increased mortality, impaired motor control, fragmented sleep, and increased neuronal cell death. TBI results in significant changes in the transcriptome, including up-regulation of genes encoding antimicrobial peptides (AMPs). To test the in vivo functional role of these changes, we examined TBI-dependent behavior and lethality in mutants of the master immune regulator NF-κB, important for AMP induction, and found that while sleep and motor function effects were reduced, lethality effects were enhanced. Similarly, loss of most AMP classes also renders flies susceptible to lethal TBI effects. These studies validate a new Drosophila TBI model and identify immune pathways as in vivo mediators of TBI effects. Traumatic brain injury in Drosophila causes sleep and motor impairments, as well as a strong activation of the innate immune response that is crucial for survival. This study leverages Drosophila as a model organism to reveal neuroprotective and neurotoxic injury mechanisms more quickly using high throughout approaches.
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Affiliation(s)
- Bart van Alphen
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Samuel Stewart
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Marta Iwanaszko
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
- Department of Preventive Medicine—Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Fangke Xu
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Keyin Li
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Sydney Rozenfeld
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Anujaianthi Ramakrishnan
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Taichi Q. Itoh
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Shiju Sisobhan
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Zuoheng Qin
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Bridget C. Lear
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Ravi Allada
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
- * E-mail:
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Tsuji J, Thomson T, Brown C, Ghosh S, Theurkauf WE, Weng Z, Schwartz LM. Somatic piRNAs and Transposons are Differentially Expressed Coincident with Skeletal Muscle Atrophy and Programmed Cell Death. Front Genet 2022; 12:775369. [PMID: 35003216 PMCID: PMC8730325 DOI: 10.3389/fgene.2021.775369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/30/2021] [Indexed: 12/02/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small single-stranded RNAs that can repress transposon expression via epigenetic silencing and transcript degradation. They have been identified predominantly in the ovary and testis, where they serve essential roles in transposon silencing in order to protect the integrity of the genome in the germline. The potential expression of piRNAs in somatic cells has been controversial. In the present study we demonstrate the expression of piRNAs derived from both genic and transposon RNAs in the intersegmental muscles (ISMs) from the tobacco hawkmoth Manduca sexta. These piRNAs are abundantly expressed, ∼27 nt long, map antisense to transposons, are oxidation resistant, exhibit a 5’ uridine bias, and amplify via the canonical ping-pong pathway. An RNA-seq analysis demonstrated that 19 piRNA pathway genes are expressed in the ISMs and are developmentally regulated. The abundance of piRNAs does not change when the muscles initiate developmentally-regulated atrophy, but are repressed coincident with the commitment of the muscles undergo programmed cell death at the end of metamorphosis. This change in piRNA expression is correlated with the repression of several retrotransposons and the induction of specific DNA transposons. The developmentally-regulated changes in the expression of piRNAs, piRNA pathway genes, and transposons are all regulated by 20-hydroxyecdysone, the steroid hormone that controls the timing of ISM death. Taken together, these data provide compelling evidence for the existence of piRNA in somatic tissues and suggest that they may play roles in developmental processes such as programmed cell death.
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Affiliation(s)
- Junko Tsuji
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Travis Thomson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States.,Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Christine Brown
- Department of Biology, University of Massachusetts, Amherst, MA, United States
| | - Subhanita Ghosh
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, United States
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Lawrence M Schwartz
- Department of Biology, University of Massachusetts, Amherst, MA, United States
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