1
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Siddiqui NU, Karaiskakis A, Goldman AL, Eagle WVI, Low TCH, Luo H, Smibert CA, Gavis ER, Lipshitz HD. Smaug regulates germ plasm assembly and primordial germ cell number in Drosophila embryos. SCIENCE ADVANCES 2024; 10:eadg7894. [PMID: 38608012 PMCID: PMC11014450 DOI: 10.1126/sciadv.adg7894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
During Drosophila oogenesis, the Oskar (OSK) RNA binding protein (RBP) determines the amount of germ plasm that assembles at the posterior pole of the oocyte. Here, we identify mechanisms that subsequently regulate germ plasm assembly in the early embryo. We show that the Smaug (SMG) RBP is transported into the germ plasm of the early embryo where it accumulates in the germ granules. SMG binds to and represses translation of the osk messenger RNA (mRNA) as well as the bruno 1 (bru1) mRNA, which encodes an RBP that we show promotes germ plasm production. Loss of SMG or mutation of SMG's binding sites in the osk or bru1 mRNA results in excess translation of these transcripts in the germ plasm, accumulation of excess germ plasm, and budding of excess primordial germ cells (PGCs). Therefore, SMG triggers a posttranscriptional regulatory pathway that attenuates the amount of germ plasm in embryos to modulate the number of PGCs.
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Affiliation(s)
- Najeeb U. Siddiqui
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
- Program in Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Angelo Karaiskakis
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Aaron L. Goldman
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
- Program in Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Whitby V. I. Eagle
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Timothy C. H. Low
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Hua Luo
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Craig A. Smibert
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Elizabeth R. Gavis
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Howard D. Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
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2
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Salgania HK, Metz J, Jeske M. ReLo is a simple and rapid colocalization assay to identify and characterize direct protein-protein interactions. Nat Commun 2024; 15:2875. [PMID: 38570497 PMCID: PMC10991417 DOI: 10.1038/s41467-024-47233-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
The characterization of protein-protein interactions (PPIs) is fundamental to the understanding of biochemical processes. Many methods have been established to identify and study direct PPIs; however, screening and investigating PPIs involving large or poorly soluble proteins remains challenging. Here, we introduce ReLo, a simple, rapid, and versatile cell culture-based method for detecting and investigating interactions in a cellular context. Our experiments demonstrate that ReLo specifically detects direct binary PPIs. Furthermore, we show that ReLo bridging experiments can also be used to determine the binding topology of subunits within multiprotein complexes. In addition, ReLo facilitates the identification of protein domains that mediate complex formation, allows screening for interfering point mutations, and it is sensitive to drugs that mediate or disrupt an interaction. In summary, ReLo is a simple and rapid alternative for the study of PPIs, especially when studying structurally complex proteins or when established methods fail.
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Affiliation(s)
- Harpreet Kaur Salgania
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Jutta Metz
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Mandy Jeske
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
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3
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Denessiouk K, Denesyuk AI, Permyakov SE, Permyakov EA, Johnson MS, Uversky VN. The active site of the SGNH hydrolase-like fold proteins: Nucleophile-oxyanion (Nuc-Oxy) and Acid-Base zones. Curr Res Struct Biol 2023; 7:100123. [PMID: 38235349 PMCID: PMC10792757 DOI: 10.1016/j.crstbi.2023.100123] [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: 10/26/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024] Open
Abstract
SGNH hydrolase-like fold proteins are serine proteases with the default Asp-His-Ser catalytic triad. Here, we show that these proteins share two unique conserved structural organizations around the active site: (1) the Nuc-Oxy Zone around the catalytic nucleophile and the oxyanion hole, and (2) the Acid-Base Zone around the catalytic acid and base. The Nuc-Oxy Zone consists of 14 amino acids cross-linked with eight conserved intra- and inter-block hydrogen bonds. The Acid-Base Zone is constructed from a single fragment of the polypeptide chain, which incorporates both the catalytic acid and base, and whose N- and C-terminal residues are linked together by a conserved hydrogen bond. The Nuc-Oxy and Acid-Base Zones are connected by an SHLink, a two-bond conserved interaction from amino acids, adjacent to the catalytic nucleophile and base.
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Affiliation(s)
- Konstantin Denessiouk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290, Russia
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku, 20520, Finland
| | - Alexander I. Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290, Russia
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku, 20520, Finland
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290, Russia
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290, Russia
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku, 20520, Finland
| | - Vladimir N. Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290, Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
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4
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Lin Y, Suyama R, Kawaguchi S, Iki T, Kai T. Tejas functions as a core component in nuage assembly and precursor processing in Drosophila piRNA biogenesis. J Cell Biol 2023; 222:e202303125. [PMID: 37555815 PMCID: PMC10412688 DOI: 10.1083/jcb.202303125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/11/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs), which protect genome from the attack by transposons, are produced and amplified in membraneless granules called nuage. In Drosophila, PIWI family proteins, Tudor-domain-containing (Tdrd) proteins, and RNA helicases are assembled and form nuage to ensure piRNA production. However, the molecular functions of the Tdrd protein Tejas (Tej) in piRNA biogenesis remain unknown. Here, we conduct a detailed analysis of the subcellular localization of fluorescently tagged nuage proteins and behavior of piRNA precursors. Our results demonstrate that Tej functions as a core component that recruits Vasa (Vas) and Spindle-E (Spn-E) into nuage granules through distinct motifs, thereby assembling nuage and engaging precursors for further processing. Our study also reveals that the low-complexity region of Tej regulates the mobility of Vas. Based on these results, we propose that Tej plays a pivotal role in piRNA precursor processing by assembling Vas and Spn-E into nuage and modulating the mobility of nuage components.
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Affiliation(s)
- Yuxuan Lin
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Ritsuko Suyama
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | - Taichiro Iki
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Toshie Kai
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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5
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Doyle DA, Burian FN, Aharoni B, Klinder AJ, Menzel MM, Nifras GCC, Shabazz-Henry AL, Palma BU, Hidalgo GA, Sottolano CJ, Ortega BM, Niepielko MG. Germ Granule Evolution Provides Mechanistic Insight into Drosophila Germline Development. Mol Biol Evol 2023; 40:msad174. [PMID: 37527522 PMCID: PMC10414811 DOI: 10.1093/molbev/msad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023] Open
Abstract
The copackaging of mRNAs into biomolecular condensates called germ granules is a conserved strategy to posttranscriptionally regulate germline mRNAs. In Drosophila melanogaster, mRNAs accumulate in germ granules by forming homotypic clusters, aggregates containing multiple transcripts from the same gene. Nucleated by Oskar (Osk), homotypic clusters are generated through a stochastic seeding and self-recruitment process that requires the 3' untranslated region (UTR) of germ granule mRNAs. Interestingly, the 3' UTR belonging to germ granule mRNAs, such as nanos (nos), have considerable sequence variations among Drosophila species and we hypothesized that this diversity influences homotypic clustering. To test our hypothesis, we investigated the homotypic clustering of nos and polar granule component (pgc) in four Drosophila species and concluded that clustering is a conserved process used to enrich germ granule mRNAs. However, we discovered germ granule phenotypes that included significant changes in the abundance of transcripts present in species' homotypic clusters, which also reflected diversity in the number of coalesced primordial germ cells within their embryonic gonads. By integrating biological data with computational modeling, we found that multiple mechanisms underlie naturally occurring germ granule diversity, including changes in nos, pgc, osk levels and/or homotypic clustering efficacy. Furthermore, we demonstrated how the nos 3' UTR from different species influences nos clustering, causing granules to have ∼70% less nos and increasing the presence of defective primordial germ cells. Our results highlight the impact that evolution has on germ granules, which should provide broader insight into processes that modify compositions and activities of other classes of biomolecular condensate.
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Affiliation(s)
- Dominique A Doyle
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Florencia N Burian
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Benjamin Aharoni
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Annabelle J Klinder
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Melissa M Menzel
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | | | | | - Bianca Ulrich Palma
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Gisselle A Hidalgo
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Christopher J Sottolano
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, USA
| | - Bianca M Ortega
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Matthew G Niepielko
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
- Department of Biological Sciences, Kean University, Union, NJ, USA
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6
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Curnutte HA, Lan X, Sargen M, Ao Ieong SM, Campbell D, Kim H, Liao Y, Lazar SB, Trcek T. Proteins rather than mRNAs regulate nucleation and persistence of Oskar germ granules in Drosophila. Cell Rep 2023; 42:112723. [PMID: 37384531 PMCID: PMC10439980 DOI: 10.1016/j.celrep.2023.112723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/24/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023] Open
Abstract
RNA granules are membraneless condensates that provide functional compartmentalization within cells. The mechanisms by which RNA granules form are under intense investigation. Here, we characterize the role of mRNAs and proteins in the formation of germ granules in Drosophila. Super-resolution microscopy reveals that the number, size, and distribution of germ granules is precisely controlled. Surprisingly, germ granule mRNAs are not required for the nucleation or the persistence of germ granules but instead control their size and composition. Using an RNAi screen, we determine that RNA regulators, helicases, and mitochondrial proteins regulate germ granule number and size, while the proteins of the endoplasmic reticulum, nuclear pore complex, and cytoskeleton control their distribution. Therefore, the protein-driven formation of Drosophila germ granules is mechanistically distinct from the RNA-dependent condensation observed for other RNA granules such as stress granules and P-bodies.
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Affiliation(s)
- Harrison A Curnutte
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Xinyue Lan
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Manuel Sargen
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Si Man Ao Ieong
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Dylan Campbell
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Hyosik Kim
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Yijun Liao
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Sarah Bailah Lazar
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Tatjana Trcek
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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7
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Siddiqui NU, Karaiskakis A, Goldman AL, Eagle WV, Smibert CA, Gavis ER, Lipshitz HD. Smaug regulates germ plasm synthesis and primordial germ cell number in Drosophila embryos by repressing the oskar and bruno 1 mRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530189. [PMID: 36909513 PMCID: PMC10002672 DOI: 10.1101/2023.02.27.530189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
During Drosophila oogenesis, the Oskar (OSK) RNA-binding protein (RBP) determines the amount of germ plasm that assembles at the posterior pole of the oocyte. Here we identify the mechanisms that regulate the osk mRNA in the early embryo. We show that the Smaug (SMG) RBP is transported into the germ plasm of the early embryo where it accumulates in the germ granules. SMG binds to and represses translation of the osk mRNA itself as well as the bruno 1 (bru1) mRNA, which encodes an RBP that we show promotes germ plasm production. Loss of SMG or mutation of SMG's binding sites in the osk or bru1 mRNAs results in ectopic translation of these transcripts in the germ plasm and excess PGCs. SMG therefore triggers a post-transcriptional regulatory pathway that attenuates germ plasm synthesis in embryos, thus modulating the number of PGCs.
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Affiliation(s)
- Najeeb U. Siddiqui
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
- Program in Developmental & Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Angelo Karaiskakis
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
| | - Aaron L. Goldman
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
- Program in Developmental & Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Whitby V.I. Eagle
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Craig A. Smibert
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
| | - Elizabeth R. Gavis
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Howard D. Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
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8
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Chiappetta A, Liao J, Tian S, Trcek T. Structural and functional organization of germ plasm condensates. Biochem J 2022; 479:2477-2495. [PMID: 36534469 PMCID: PMC10722471 DOI: 10.1042/bcj20210815] [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: 09/09/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 12/23/2022]
Abstract
Reproductive success of metazoans relies on germ cells. These cells develop early during embryogenesis, divide and undergo meiosis in the adult to make sperm and oocytes. Unlike somatic cells, germ cells are immortal and transfer their genetic material to new generations. They are also totipotent, as they differentiate into different somatic cell types. The maintenance of immortality and totipotency of germ cells depends on extensive post-transcriptional and post-translational regulation coupled with epigenetic remodeling, processes that begin with the onset of embryogenesis [1, 2]. At the heart of this regulation lie germ granules, membraneless ribonucleoprotein condensates that are specific to the germline cytoplasm called the germ plasm. They are a hallmark of all germ cells and contain several proteins and RNAs that are conserved across species. Interestingly, germ granules are often structured and tend to change through development. In this review, we describe how the structure of germ granules becomes established and discuss possible functional outcomes these structures have during development.
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9
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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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10
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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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11
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Lachke SA. RNA-binding proteins and post-transcriptional regulation in lens biology and cataract: Mediating spatiotemporal expression of key factors that control the cell cycle, transcription, cytoskeleton and transparency. Exp Eye Res 2022; 214:108889. [PMID: 34906599 PMCID: PMC8792301 DOI: 10.1016/j.exer.2021.108889] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 01/03/2023]
Abstract
Development of the ocular lens - a transparent tissue capable of sustaining frequent shape changes for optimal focusing power - pushes the boundaries of what cells can achieve using the molecular toolkit encoded by their genomes. The mammalian lens contains broadly two types of cells, the anteriorly located monolayer of epithelial cells which, at the equatorial region of the lens, initiate differentiation into fiber cells that contribute to the bulk of the tissue. This differentiation program involves massive upregulation of select fiber cell-expressed RNAs and their subsequent translation into high amounts of proteins, such as crystallins. But intriguingly, fiber cells achieve this while also simultaneously undergoing significant morphological changes such as elongation - involving about 1000-fold length-wise increase - and migration, which requires modulation of cytoskeletal and cell adhesion factors. Adding further to the challenges, these molecular and cellular events have to be coordinated as fiber cells progress toward loss of their nuclei and organelles, which irreversibly compromises their potential for harnessing genetically hardwired information. A long-standing question is how processes downstream of signaling and transcription, which may also participate in feedback regulation, contribute toward orchestrating these cellular differentiation events in the lens. It is now becoming clear from findings over the past decade that post-transcriptional gene expression regulatory mechanisms are critical in controlling cellular proteomes and coordinating key processes in lens development and fiber cell differentiation. Indeed, RNA-binding proteins (RBPs) such as Caprin2, Celf1, Rbm24 and Tdrd7 have now been described in mediating post-transcriptional control over key factors (e.g. Actn2, Cdkn1a (p21Cip1), Cdkn1b (p27Kip1), various crystallins, Dnase2b, Hspb1, Pax6, Prox1, Sox2) that are variously involved in cell cycle, transcription, cytoskeleton maintenance and differentiation in the lens. Furthermore, deficiencies of these RBPs have been shown to result in various eye and lens defects and/or cataract. Because fiber cell differentiation in the lens occurs throughout life, the underlying regulatory mechanisms operational in development are expected to also be recruited for the maintenance of transparency in aged lenses. Indeed, in support of this, TDRD7 and CAPRIN2 loci have been linked to age-related cataract in humans. Here, I will review the role of key RBPs in the lens and their importance in understanding the pathology of lens defects. I will discuss advances in RBP-based gene expression control, in general, and the important challenges that need to be addressed in the lens to define the mechanisms that determine the epithelial and fiber cell proteome. Finally, I will also discuss in detail several key future directions including the application of bioinformatics approaches such as iSyTE to study RBP-based post-transcriptional gene expression control in the aging lens and in the context of age-related cataract.
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Affiliation(s)
- Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA; Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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12
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Xu C, Cao Y, Bao J. Building RNA-protein germ granules: insights from the multifaceted functions of DEAD-box helicase Vasa/Ddx4 in germline development. Cell Mol Life Sci 2021; 79:4. [PMID: 34921622 PMCID: PMC11072811 DOI: 10.1007/s00018-021-04069-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023]
Abstract
The segregation and maintenance of a dedicated germline in multicellular organisms is essential for species propagation in the sexually reproducing metazoan kingdom. The germline is distinct from somatic cells in that it is ultimately dedicated to acquiring the "totipotency" and to regenerating the offspring after fertilization. The most striking feature of germ cells lies in the presence of characteristic membraneless germ granules that have recently proven to behave like liquid droplets resulting from liquid-liquid phase separation (LLPS). Vasa/Ddx4, a faithful DEAD-box family germline marker highly conserved across metazoan species, harbors canonical DEAD-box motifs and typical intrinsically disordered sequences at both the N-terminus and C-terminus. This feature enables it to serve as a primary driving force behind germ granule formation and helicase-mediated RNA metabolism (e.g., piRNA biogenesis). Genetic ablation of Vasa/Ddx4 or the catalytic-dead mutations abolishing its helicase activity led to sexually dimorphic germline defects resulting in either male or female sterility among diverse species. While recent efforts have discovered pivotal functions of Vasa/Ddx4 in somatic cells, especially in multipotent stem cells, we herein summarize the helicase-dependent and -independent functions of Vasa/Ddx4 in the germline, and discuss recent findings of Vasa/Ddx4-mediated phase separation, germ granule formation and piRNA-dependent retrotransposon control essential for germline development.
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Affiliation(s)
- Caoling Xu
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, China
| | - Yuzhu Cao
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, China
| | - Jianqiang Bao
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, China.
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13
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Mercer M, Jang S, Ni C, Buszczak M. The Dynamic Regulation of mRNA Translation and Ribosome Biogenesis During Germ Cell Development and Reproductive Aging. Front Cell Dev Biol 2021; 9:710186. [PMID: 34805139 PMCID: PMC8595405 DOI: 10.3389/fcell.2021.710186] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/07/2021] [Indexed: 01/21/2023] Open
Abstract
The regulation of mRNA translation, both globally and at the level of individual transcripts, plays a central role in the development and function of germ cells across species. Genetic studies using flies, worms, zebrafish and mice have highlighted the importance of specific RNA binding proteins in driving various aspects of germ cell formation and function. Many of these mRNA binding proteins, including Pumilio, Nanos, Vasa and Dazl have been conserved through evolution, specifically mark germ cells, and carry out similar functions across species. These proteins typically influence mRNA translation by binding to specific elements within the 3′ untranslated region (UTR) of target messages. Emerging evidence indicates that the global regulation of mRNA translation also plays an important role in germ cell development. For example, ribosome biogenesis is often regulated in a stage specific manner during gametogenesis. Moreover, oocytes need to produce and store a sufficient number of ribosomes to support the development of the early embryo until the initiation of zygotic transcription. Accumulating evidence indicates that disruption of mRNA translation regulatory mechanisms likely contributes to infertility and reproductive aging in humans. These findings highlight the importance of gaining further insights into the mechanisms that control mRNA translation within germ cells. Future work in this area will likely have important impacts beyond germ cell biology.
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Affiliation(s)
- Marianne Mercer
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Seoyeon Jang
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Chunyang Ni
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Michael Buszczak
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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14
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Price IF, Hertz HL, Pastore B, Wagner J, Tang W. Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans. eLife 2021; 10:e72276. [PMID: 34730513 PMCID: PMC8616582 DOI: 10.7554/elife.72276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 11/01/2021] [Indexed: 11/30/2022] Open
Abstract
The germ line produces gametes that transmit genetic and epigenetic information to the next generation. Maintenance of germ cells and development of gametes require germ granules-well-conserved membraneless and RNA-rich organelles. The composition of germ granules is elusive owing to their dynamic nature and their exclusive expression in the germ line. Using Caenorhabditis elegans germ granule, called P granule, as a model system, we employed a proximity-based labeling method in combination with mass spectrometry to comprehensively define its protein components. This set of experiments identified over 200 proteins, many of which contain intrinsically disordered regions (IDRs). An RNA interference-based screen identified factors that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two putative LOTUS-domain proteins. Loss of eggd-1 and eggd-2 results in separation of P granules from the nuclear envelope, germline atrophy, and reduced fertility. We show that IDRs of EGGD-1 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS domains are required to promote the perinuclear localization of P granules. Taken together, our work expands the repertoire of P granule constituents and provides new insights into the role of LOTUS-domain proteins in germ granule organization.
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Affiliation(s)
- Ian F Price
- Department of Biological Chemistry and PharmacologyColumbusUnited States
- Center for RNA BiologyColumbusUnited States
- Ohio State Biochemistry ProgramColumbusUnited States
| | - Hannah L Hertz
- Department of Biological Chemistry and PharmacologyColumbusUnited States
- Center for RNA BiologyColumbusUnited States
| | - Benjamin Pastore
- Department of Biological Chemistry and PharmacologyColumbusUnited States
- Center for RNA BiologyColumbusUnited States
- Ohio State Biochemistry ProgramColumbusUnited States
| | - Jillian Wagner
- Department of Biological Chemistry and PharmacologyColumbusUnited States
- Department of Molecular Genetics, Ohio State UniversityColumbusUnited States
| | - Wen Tang
- Department of Biological Chemistry and PharmacologyColumbusUnited States
- Center for RNA BiologyColumbusUnited States
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15
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Perera RP, Shaikhqasem A, Rostam N, Dickmanns A, Ficner R, Tittmann K, Dosch R. Bucky Ball Is a Novel Zebrafish Vasa ATPase Activator. Biomolecules 2021; 11:1507. [PMID: 34680140 PMCID: PMC8533965 DOI: 10.3390/biom11101507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022] Open
Abstract
Many multicellular organisms specify germ cells during early embryogenesis by the inheritance of ribonucleoprotein (RNP) granules known as germplasm. However, the role of complex interactions of RNP granules during germ cell specification remains elusive. This study characterizes the interaction of RNP granules, Buc, and zebrafish Vasa (zfVasa) during germ cell specification. We identify a novel zfVasa-binding motif (Buc-VBM) in Buc and a Buc-binding motif (zfVasa-BBM) in zfVasa. Moreover, we show that Buc and zfVasa directly bind in vitro and that this interaction is independent of the RNA. Our circular dichroism spectroscopy data reveal that the intrinsically disordered Buc-VBM peptide forms alpha-helices in the presence of the solvent trifluoroethanol. Intriguingly, we further demonstrate that Buc-VBM enhances zfVasa ATPase activity, thereby annotating the first biochemical function of Buc as a zfVasa ATPase activator. Collectively, these results propose a model in which the activity of zfVasa is a central regulator of primordial germ cell (PGC) formation and is tightly controlled by the germplasm organizer Buc.
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Affiliation(s)
| | - Alaa Shaikhqasem
- Department for Molecular Structural Biology, University of Goettingen, 37077 Goettingen, Germany; (A.S.); (A.D.); (R.F.)
| | - Nadia Rostam
- Institute for Human Genetics, University of Goettingen, 37073 Goettingen, Germany;
| | - Achim Dickmanns
- Department for Molecular Structural Biology, University of Goettingen, 37077 Goettingen, Germany; (A.S.); (A.D.); (R.F.)
| | - Ralf Ficner
- Department for Molecular Structural Biology, University of Goettingen, 37077 Goettingen, Germany; (A.S.); (A.D.); (R.F.)
- deCluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), University of Goettingen, 37073 Goettingen, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, University of Goettingen, 37077 Goettingen, Germany;
| | - Roland Dosch
- Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany;
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16
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Blondel L, Besse S, Rivard EL, Ylla G, Extavour CG. Evolution of a cytoplasmic determinant: evidence for the biochemical basis of functional evolution of the novel germ line regulator oskar. Mol Biol Evol 2021; 38:5491-5513. [PMID: 34550378 PMCID: PMC8662646 DOI: 10.1093/molbev/msab284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Germ line specification is essential in sexually reproducing organisms. Despite their critical role, the evolutionary history of the genes that specify animal germ cells is heterogeneous and dynamic. In many insects, the gene oskar is required for the specification of the germ line. However, the germ line role of oskar is thought to be a derived role resulting from co-option from an ancestral somatic role. To address how evolutionary changes in protein sequence could have led to changes in the function of Oskar protein that enabled it to regulate germ line specification, we searched for oskar orthologs in 1,565 publicly available insect genomic and transcriptomic data sets. The earliest-diverging lineage in which we identified an oskar ortholog was the order Zygentoma (silverfish and firebrats), suggesting that oskar originated before the origin of winged insects. We noted some order-specific trends in oskar sequence evolution, including whole gene duplications, clade-specific losses, and rapid divergence. An alignment of all known 379 Oskar sequences revealed new highly conserved residues as candidates that promote dimerization of the LOTUS domain. Moreover, we identified regions of the OSK domain with conserved predicted RNA binding potential. Furthermore, we show that despite a low overall amino acid conservation, the LOTUS domain shows higher conservation of predicted secondary structure than the OSK domain. Finally, we suggest new key amino acids in the LOTUS domain that may be involved in the previously reported Oskar−Vasa physical interaction that is required for its germ line role.
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Affiliation(s)
- Leo Blondel
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Savandara Besse
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Emily L Rivard
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Guillem Ylla
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Cassandra G Extavour
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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17
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Cipriani PG, Bay O, Zinno J, Gutwein M, Gan HH, Mayya VK, Chung G, Chen JX, Fahs H, Guan Y, Duchaine TF, Selbach M, Piano F, Gunsalus KC. Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules. eLife 2021; 10:60833. [PMID: 34223818 PMCID: PMC8331183 DOI: 10.7554/elife.60833] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 06/27/2021] [Indexed: 12/16/2022] Open
Abstract
We describe MIP-1 and MIP-2, novel paralogous C. elegans germ granule components that interact with the intrinsically disordered MEG-3 protein. These proteins promote P granule condensation, form granules independently of MEG-3 in the postembryonic germ line, and balance each other in regulating P granule growth and localization. MIP-1 and MIP-2 each contain two LOTUS domains and intrinsically disordered regions and form homo- and heterodimers. They bind and anchor the Vasa homolog GLH-1 within P granules and are jointly required for coalescence of MEG-3, GLH-1, and PGL proteins. Animals lacking MIP-1 and MIP-2 show temperature-sensitive embryonic lethality, sterility, and mortal germ lines. Germline phenotypes include defects in stem cell self-renewal, meiotic progression, and gamete differentiation. We propose that these proteins serve as scaffolds and organizing centers for ribonucleoprotein networks within P granules that help recruit and balance essential RNA processing machinery to regulate key developmental transitions in the germ line.
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Affiliation(s)
- Patricia Giselle Cipriani
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States.,NYU Abu Dhabi Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Olivia Bay
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - John Zinno
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Michelle Gutwein
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Hin Hark Gan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Vinay K Mayya
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Canada
| | - George Chung
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Jia-Xuan Chen
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Hala Fahs
- NYU Abu Dhabi Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Yu Guan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Thomas F Duchaine
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Fabio Piano
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States.,NYU Abu Dhabi Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kristin C Gunsalus
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States.,NYU Abu Dhabi Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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18
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Receptor-mediated yolk uptake is required for oskar mRNA localization and cortical anchorage of germ plasm components in the Drosophila oocyte. PLoS Biol 2021; 19:e3001183. [PMID: 33891588 PMCID: PMC8064586 DOI: 10.1371/journal.pbio.3001183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/11/2021] [Indexed: 11/22/2022] Open
Abstract
The Drosophila germ plasm is responsible for germ cell formation. Its assembly begins with localization of oskar mRNA to the posterior pole of the oocyte. The oskar translation produces 2 isoforms with distinct functions: short Oskar recruits germ plasm components, whereas long Oskar remodels actin to anchor the components to the cortex. The mechanism by which long Oskar anchors them remains elusive. Here, we report that Yolkless, which facilitates uptake of nutrient yolk proteins into the oocyte, is a key cofactor for long Oskar. Loss of Yolkless or depletion of yolk proteins disrupts the microtubule alignment and oskar mRNA localization at the posterior pole of the oocyte, whereas microtubule-dependent localization of bicoid mRNA to the anterior and gurken mRNA to the anterior-dorsal corner remains intact. Furthermore, these mutant oocytes do not properly respond to long Oskar, causing defects in the actin remodeling and germ plasm anchoring. Thus, the yolk uptake is not merely the process for nutrient incorporation, but also crucial for oskar mRNA localization and cortical anchorage of germ plasm components in the oocyte. A study of the fruit fly Drosophila reveals that receptor-mediated yolk uptake is not merely a nutrient storage process for future embryogenesis, but is also required for localization of Oskar mRNA and cortical anchorage of germ plasm components in the oocyte during oogenesis.
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19
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Filanti B, Piccinini G, Bettini S, Lazzari M, Franceschini V, Maurizii MG, Milani L. Early germline differentiation in bivalves: TDRD7 as a candidate investigational unit for Ruditapes philippinarum germ granule assembly. Histochem Cell Biol 2021; 156:19-34. [PMID: 33770286 PMCID: PMC8277629 DOI: 10.1007/s00418-021-01983-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2021] [Indexed: 01/23/2023]
Abstract
The germline is a key feature of sexual animals and the ways in which it separates from the soma differ widely across Metazoa. However, at least at some point during germline differentiation, some cytoplasmic supramolecular structures (collectively called germ plasm-related structures) are present and involved in its specification and/or differentiation. The factors involved in the assembly of these granular structures are various and non-ubiquitous among animals, even if some functional patterns and the presence of certain domains appear to be shared among some. For instance, the LOTUS domain is shared by Oskar, the Holometabola germ plasm master regulator, and some Tudor-family proteins assessed as being involved in the proper assembly of germ granules of different animals. Here, we looked for the presence of LOTUS-containing proteins in the transcriptome of Ruditapes philippinarum (Bivalvia). Such species is of particular interest because it displays annual renewal of gonads, sided by the renewal of germline differentiation pathways. Moreover, previous works have identified in its early germ cells cytoplasmic granules containing germline determinants. We selected the orthologue of TDRD7 as a candidate involved in the early steps of germline differentiation through bioinformatic predictions and immunohistological patterning (immunohistochemistry and immunofluorescence). We observed the expression of the protein in putative precursors of germline cells, upstream to the germline marker Vasa. This, added to the fact that orthologues of this protein are involved in the assembly of germ granules in mouse, zebrafish, and fly, makes it a worthy study unit for investigations on the formation of such structures in bivalves.
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Affiliation(s)
- Beatrice Filanti
- Department of Biological, Geological and Environmental Sciences, BiGeA, University of Bologna, Bologna, Italy
| | - Giovanni Piccinini
- Department of Biological, Geological and Environmental Sciences, BiGeA, University of Bologna, Bologna, Italy
| | - Simone Bettini
- Department of Biological, Geological and Environmental Sciences, BiGeA, University of Bologna, Bologna, Italy
| | - Maurizio Lazzari
- Department of Biological, Geological and Environmental Sciences, BiGeA, University of Bologna, Bologna, Italy
| | - Valeria Franceschini
- Department of Biological, Geological and Environmental Sciences, BiGeA, University of Bologna, Bologna, Italy
| | - Maria Gabriella Maurizii
- Department of Biological, Geological and Environmental Sciences, BiGeA, University of Bologna, Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological and Environmental Sciences, BiGeA, University of Bologna, Bologna, Italy.
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20
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Anand D, Al Saai S, Shrestha SK, Barnum CE, Chuma S, Lachke SA. Genome-Wide Analysis of Differentially Expressed miRNAs and Their Associated Regulatory Networks in Lenses Deficient for the Congenital Cataract-Linked Tudor Domain Containing Protein TDRD7. Front Cell Dev Biol 2021; 9:615761. [PMID: 33665188 PMCID: PMC7921330 DOI: 10.3389/fcell.2021.615761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/27/2021] [Indexed: 12/15/2022] Open
Abstract
Mutations/deficiency of TDRD7, encoding a tudor domain protein involved in post-transcriptional gene expression control, causes early onset cataract in humans. While Tdrd7 is implicated in the control of key lens mRNAs, the impact of Tdrd7 deficiency on microRNAs (miRNAs) and how this contributes to transcriptome misexpression and to cataracts, is undefined. We address this critical knowledge-gap by investigating Tdrd7-targeted knockout (Tdrd7-/-) mice that exhibit fully penetrant juvenile cataracts. We performed Affymetrix miRNA 3.0 microarray analysis on Tdrd7-/- mouse lenses at postnatal day (P) 4, a stage preceding cataract formation. This analysis identifies 22 miRNAs [14 over-expressed (miR-15a, miR-19a, miR-138, miR-328, miR-339, miR-345, miR-378b, miR-384, miR-467a, miR-1224, miR-1935, miR-1946a, miR-3102, miR-3107), 8 reduced (let-7b, miR-34c, miR-298, miR-382, miR-409, miR-1198, miR-1947, miR-3092)] to be significantly misexpressed (fold-change ≥ ± 1.2, p-value < 0.05) in Tdrd7-/- lenses. To understand how these misexpressed miRNAs impact Tdrd7-/- cataract, we predicted their mRNA targets and examined their misexpression upon Tdrd7-deficiency by performing comparative transcriptomics analysis on P4 and P30 Tdrd7-/- lens. To prioritize these target mRNAs, we used various stringency filters (e.g., fold-change in Tdrd7-/- lens, iSyTE-based lens-enriched expression) and identified 98 reduced and 89 elevated mRNA targets for overexpressed and reduced miRNAs, respectively, which were classified as “top-priority” “high-priority,” and “promising” candidates. For Tdrd7-/- lens overexpressed miRNAs, this approach identified 18 top-priority reduced target mRNAs: Alad, Ankrd46, Ceacam10, Dgat2, Ednrb, H2-Eb1, Klhl22, Lin7a, Loxl1, Lpin1, Npc1, Olfm1, Ppm1e, Ppp1r1a, Rgs8, Shisa4, Snx22 and Wnk2. Majority of these targets were also altered in other gene-specific perturbation mouse models (e.g., Brg1, E2f1/E2f2/E2f3, Foxe3, Hsf4, Klf4, Mafg/Mafk, Notch) of lens defects/cataract, suggesting their importance to lens biology. Gene ontology (GO) provided further insight into their relevance to lens pathology. For example, the Tdrd7-deficient lens capsule defect may be explained by reduced mRNA targets (e.g., Col4a3, Loxl1, Timp2, Timp3) associated with “basement membrane”. GO analysis also identified new genes (e.g., Casz1, Rasgrp1) recently linked to lens biology/pathology. Together, these analyses define a new Tdrd7-downstream miRNA-mRNA network, in turn, uncovering several new mRNA targets and their associated pathways relevant to lens biology and offering molecular insights into the pathology of congenital cataract.
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Affiliation(s)
- Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Salma Al Saai
- Department of Biological Sciences, University of Delaware, Newark, DE, United States.,Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, United States
| | - Sanjaya K Shrestha
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Shinichiro Chuma
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, United States.,Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, United States
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21
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Donsbach P, Klostermeier D. Regulation of RNA helicase activity: principles and examples. Biol Chem 2021; 402:529-559. [PMID: 33583161 DOI: 10.1515/hsz-2020-0362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
RNA helicases are a ubiquitous class of enzymes involved in virtually all processes of RNA metabolism, from transcription, mRNA splicing and export, mRNA translation and RNA transport to RNA degradation. Although ATP-dependent unwinding of RNA duplexes is their hallmark reaction, not all helicases catalyze unwinding in vitro, and some in vivo functions do not depend on duplex unwinding. RNA helicases are divided into different families that share a common helicase core with a set of helicase signature motives. The core provides the active site for ATP hydrolysis, a binding site for non-sequence-specific interaction with RNA, and in many cases a basal unwinding activity. Its activity is often regulated by flanking domains, by interaction partners, or by self-association. In this review, we summarize the regulatory mechanisms that modulate the activities of the helicase core. Case studies on selected helicases with functions in translation, splicing, and RNA sensing illustrate the various modes and layers of regulation in time and space that harness the helicase core for a wide spectrum of cellular tasks.
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Affiliation(s)
- Pascal Donsbach
- Institute for Physical Chemistry, University of Münster, Corrensstrasse 30, D-48149Münster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Münster, Corrensstrasse 30, D-48149Münster, Germany
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22
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Aoki ST, Lynch TR, Crittenden SL, Bingman CA, Wickens M, Kimble J. C. elegans germ granules require both assembly and localized regulators for mRNA repression. Nat Commun 2021; 12:996. [PMID: 33579952 PMCID: PMC7881195 DOI: 10.1038/s41467-021-21278-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 01/14/2021] [Indexed: 02/07/2023] Open
Abstract
Cytoplasmic RNA-protein (RNP) granules have diverse biophysical properties, from liquid to solid, and play enigmatic roles in RNA metabolism. Nematode P granules are paradigmatic liquid droplet granules and central to germ cell development. Here we analyze a key P granule scaffolding protein, PGL-1, to investigate the functional relationship between P granule assembly and function. Using a protein-RNA tethering assay, we find that reporter mRNA expression is repressed when recruited to PGL-1. We determine the crystal structure of the PGL-1 N-terminal region to 1.5 Å, discover its dimerization, and identify key residues at the dimer interface. Mutations of those interface residues prevent P granule assembly in vivo, de-repress PGL-1 tethered mRNA, and reduce fertility. Therefore, PGL-1 dimerization lies at the heart of both P granule assembly and function. Finally, we identify the P granule-associated Argonaute WAGO-1 as crucial for repression of PGL-1 tethered mRNA. We conclude that P granule function requires both assembly and localized regulators.
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Affiliation(s)
- Scott Takeo Aoki
- grid.257413.60000 0001 2287 3919Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, IN USA ,grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Tina R. Lynch
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Sarah L. Crittenden
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA ,grid.14003.360000 0001 2167 3675Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI USA
| | - Craig A. Bingman
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Marvin Wickens
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Judith Kimble
- grid.14003.360000 0001 2167 3675Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA ,grid.14003.360000 0001 2167 3675Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI USA
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23
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Mukherjee N, Mukherjee C. Germ cell ribonucleoprotein granules in different clades of life: From insects to mammals. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1642. [PMID: 33555143 DOI: 10.1002/wrna.1642] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/12/2022]
Abstract
Ribonucleoprotein (RNP) granules are no newcomers in biology. Found in all life forms, ranging across taxa, these membrane-less "organelles" have been classified into different categories based on their composition, structure, behavior, function, and localization. Broadly, they can be listed as stress granules (SGs), processing bodies (PBs), neuronal granules (NGs), and germ cell granules (GCGs). Keeping in line with the topic of this review, RNP granules present in the germ cells have been implicated in a wide range of cellular functions including cellular specification, differentiation, proliferation, and so forth. The mechanisms used by them can be diverse and many of them remain partly obscure and active areas of research. GCGs can be of different types in different organisms and at different stages of development, with multiple types coexisting in the same cell. In this review, the different known subcategories of GCGs have been studied with respect to five distinct model organisms, namely, Drosophila, Caenorhabditis elegans, Xenopus, Zebrafish, and mammals. Of them, the cytoplasmic polar granules in Drosophila, P granules in C. elegans, balbiani body in Xenopus and Zebrafish, and chromatoid bodies in mammals have been specifically emphasized upon. A descriptive account of the same has been provided along with insights into our current understanding of their functional significance with respect to cellular events relating to different developmental and reproductive processes. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Export and Localization > RNA Localization RNA in Disease and Development > RNA in Disease.
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24
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Kubíková J, Reinig R, Salgania HK, Jeske M. LOTUS-domain proteins - developmental effectors from a molecular perspective. Biol Chem 2020; 402:7-23. [DOI: 10.1515/hsz-2020-0270] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/19/2020] [Indexed: 12/15/2022]
Abstract
Abstract
The LOTUS domain (also known as OST-HTH) is a highly conserved protein domain found in a variety of bacteria and eukaryotes. In animals, the LOTUS domain is present in the proteins Oskar, TDRD5/Tejas, TDRD7/TRAP/Tapas, and MARF1/Limkain B1, all of which play essential roles in animal development, in particular during oogenesis and/or spermatogenesis. This review summarizes the diverse biological as well as molecular functions of LOTUS-domain proteins and discusses their roles as helicase effectors, post-transcriptional regulators, and critical cofactors of piRNA-mediated transcript silencing.
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Affiliation(s)
- Jana Kubíková
- Heidelberg University Biochemistry Center , Im Neuenheimer Feld 328 , D-69120 Heidelberg , Germany
| | - Rebecca Reinig
- Heidelberg University Biochemistry Center , Im Neuenheimer Feld 328 , D-69120 Heidelberg , Germany
| | - Harpreet Kaur Salgania
- Heidelberg University Biochemistry Center , Im Neuenheimer Feld 328 , D-69120 Heidelberg , Germany
| | - Mandy Jeske
- Heidelberg University Biochemistry Center , Im Neuenheimer Feld 328 , D-69120 Heidelberg , Germany
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25
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Ding D, Wei C, Dong K, Liu J, Stanton A, Xu C, Min J, Hu J, Chen C. LOTUS domain is a novel class of G-rich and G-quadruplex RNA binding domain. Nucleic Acids Res 2020; 48:9262-9272. [PMID: 32766792 PMCID: PMC7498356 DOI: 10.1093/nar/gkaa652] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/24/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
LOTUS domains are helix-turn-helix protein folds identified in essential germline proteins and are conserved in prokaryotes and eukaryotes. Despite originally predicted as an RNA binding domain, its molecular binding activity towards RNA and protein is controversial. In particular, the most conserved binding property for the LOTUS domain family remains unknown. Here, we uncovered an unexpected specific interaction of LOTUS domains with G-rich RNA sequences. Intriguingly, LOTUS domains exhibit high affinity to RNA G-quadruplex tertiary structures implicated in diverse cellular processes including piRNA biogenesis. This novel LOTUS domain-RNA interaction is conserved in bacteria, plants and animals, comprising the most ancient binding feature of the LOTUS domain family. By contrast, LOTUS domains do not preferentially interact with DNA G-quadruplexes. We further show that a subset of LOTUS domains display both RNA and protein binding activities. These findings identify the LOTUS domain as a specialized RNA binding domain across phyla and underscore the molecular mechanism underlying the function of LOTUS domain-containing proteins in RNA metabolism and regulation.
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Affiliation(s)
- Deqiang Ding
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA.,Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chao Wei
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Kunzhe Dong
- USDA Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Jiali Liu
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA.,State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Alexander Stanton
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Chao Xu
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA.,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI 49503, USA
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26
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Dodson AE, Kennedy S. Phase Separation in Germ Cells and Development. Dev Cell 2020; 55:4-17. [PMID: 33007213 DOI: 10.1016/j.devcel.2020.09.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/28/2020] [Accepted: 09/05/2020] [Indexed: 12/20/2022]
Abstract
The animal germline is an immortal cell lineage that gives rise to eggs and/or sperm each generation. Fusion of an egg and sperm, or fertilization, sets off a cascade of developmental events capable of producing an array of different cell types and body plans. How germ cells develop, function, and eventually give rise to entirely new organisms is an important question in biology. A growing body of evidence suggests that phase separation events likely play a significant and multifaceted role in germ cells and development. Here, we discuss the organization, dynamics, and potential functions of phase-separated compartments in germ cells and examine the various ways in which phase separation might contribute to the development of multicellular organisms.
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Affiliation(s)
- Anne E Dodson
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA.
| | - Scott Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
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27
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Kulkarni A, Lopez DH, Extavour CG. Shared Cell Biological Functions May Underlie Pleiotropy of Molecular Interactions in the Germ Lines and Nervous Systems of Animals. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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28
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Barnum CE, Al Saai S, Patel SD, Cheng C, Anand D, Xu X, Dash S, Siddam AD, Glazewski L, Paglione E, Polson SW, Chuma S, Mason RW, Wei S, Batish M, Fowler VM, Lachke SA. The Tudor-domain protein TDRD7, mutated in congenital cataract, controls the heat shock protein HSPB1 (HSP27) and lens fiber cell morphology. Hum Mol Genet 2020; 29:2076-2097. [PMID: 32420594 PMCID: PMC7390939 DOI: 10.1093/hmg/ddaa096] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/10/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Mutations of the RNA granule component TDRD7 (OMIM: 611258) cause pediatric cataract. We applied an integrated approach to uncover the molecular pathology of cataract in Tdrd7-/- mice. Early postnatal Tdrd7-/- animals precipitously develop cataract suggesting a global-level breakdown/misregulation of key cellular processes. High-throughput RNA sequencing integrated with iSyTE-bioinformatics analysis identified the molecular chaperone and cytoskeletal modulator, HSPB1, among high-priority downregulated candidates in Tdrd7-/- lens. A protein fluorescence two-dimensional difference in-gel electrophoresis (2D-DIGE)-coupled mass spectrometry screen also identified HSPB1 downregulation, offering independent support for its importance to Tdrd7-/- cataractogenesis. Lens fiber cells normally undergo nuclear degradation for transparency, posing a challenge: how is their cell morphology, also critical for transparency, controlled post-nuclear degradation? HSPB1 functions in cytoskeletal maintenance, and its reduction in Tdrd7-/- lens precedes cataract, suggesting cytoskeletal defects may contribute to Tdrd7-/- cataract. In agreement, scanning electron microscopy (SEM) revealed abnormal fiber cell morphology in Tdrd7-/- lenses. Further, abnormal phalloidin and wheat germ agglutinin (WGA) staining of Tdrd7-/- fiber cells, particularly those exhibiting nuclear degradation, reveals distinct regulatory mechanisms control F-actin cytoskeletal and/or membrane maintenance in post-organelle degradation maturation stage fiber cells. Indeed, RNA immunoprecipitation identified Hspb1 mRNA in wild-type lens lysate TDRD7-pulldowns, and single-molecule RNA imaging showed co-localization of TDRD7 protein with cytoplasmic Hspb1 mRNA in differentiating fiber cells, suggesting that TDRD7-ribonucleoprotein complexes may be involved in optimal buildup of key factors. Finally, Hspb1 knockdown in Xenopus causes eye/lens defects. Together, these data uncover TDRD7's novel upstream role in elevation of stress-responsive chaperones for cytoskeletal maintenance in post-nuclear degradation lens fiber cells, perturbation of which causes early-onset cataracts.
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Affiliation(s)
- Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Salma Al Saai
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shaili D Patel
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Catherine Cheng
- School of Optometry, Indiana University, Bloomington, IN 47405, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Xiaolu Xu
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Lisa Glazewski
- Nemours Biomedical Research Department, Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Emily Paglione
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shawn W Polson
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Shinichiro Chuma
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Robert W Mason
- Nemours Biomedical Research Department, Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Shuo Wei
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Velia M Fowler
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19716, USA
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29
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Tian S, Curnutte HA, Trcek T. RNA Granules: A View from the RNA Perspective. Molecules 2020; 25:E3130. [PMID: 32650583 PMCID: PMC7397151 DOI: 10.3390/molecules25143130] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/29/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
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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30
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Lasko P. Patterning the Drosophila embryo: A paradigm for RNA-based developmental genetic regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1610. [PMID: 32543002 PMCID: PMC7583483 DOI: 10.1002/wrna.1610] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/13/2020] [Accepted: 05/17/2020] [Indexed: 12/16/2022]
Abstract
Embryonic anterior–posterior patterning is established in Drosophila melanogaster by maternally expressed genes. The mRNAs of several of these genes accumulate at either the anterior or posterior pole of the oocyte via a number of mechanisms. Many of these mRNAs are also under elaborate translational regulation. Asymmetric RNA localization coupled with spatially restricted translation ensures that their proteins are restricted to the position necessary for the developmental process that they drive. Bicoid (Bcd), the anterior determinant, and Oskar (Osk), the determinant for primordial germ cells and posterior patterning, have been studied particularly closely. In early embryos an anterior–posterior gradient of Bcd is established, activating transcription of different sets of zygotic genes depending on local Bcd concentration. At the posterior pole, Osk seeds formation of polar granules, ribonucleoprotein complexes that accumulate further mRNAs and proteins involved in posterior patterning and germ cell specification. After fertilization, polar granules associate with posterior nuclei and mature into nuclear germ granules. Osk accumulates in these granules, and either by itself or as part of the granules, stimulates germ cell division. This article is categorized under:RNA Export and Localization > RNA Localization Translation > Translation Regulation RNA in Disease and Development > RNA in Development
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Affiliation(s)
- Paul Lasko
- Department of Biology, McGill University, Montréal, Québec, Canada.,Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
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31
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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: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [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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32
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Blondel L, Jones TEM, Extavour CG. Bacterial contribution to genesis of the novel germ line determinant oskar. eLife 2020; 9:e45539. [PMID: 32091394 PMCID: PMC7250577 DOI: 10.7554/elife.45539] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/23/2020] [Indexed: 12/20/2022] Open
Abstract
New cellular functions and developmental processes can evolve by modifying existing genes or creating novel genes. Novel genes can arise not only via duplication or mutation but also by acquiring foreign DNA, also called horizontal gene transfer (HGT). Here we show that HGT likely contributed to the creation of a novel gene indispensable for reproduction in some insects. Long considered a novel gene with unknown origin, oskar has evolved to fulfil a crucial role in insect germ cell formation. Our analysis of over 100 insect Oskar sequences suggests that oskar arose de novo via fusion of eukaryotic and prokaryotic sequences. This work shows that highly unusual gene origin processes can give rise to novel genes that may facilitate evolution of novel developmental mechanisms.
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Affiliation(s)
- Leo Blondel
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Tamsin EM Jones
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Cassandra G Extavour
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
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33
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Trcek T, Lehmann R. Germ granules in Drosophila. Traffic 2019; 20:650-660. [PMID: 31218815 PMCID: PMC6771631 DOI: 10.1111/tra.12674] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/26/2019] [Accepted: 06/14/2019] [Indexed: 12/22/2022]
Abstract
Germ granules are hallmarks of all germ cells. Early ultrastructural studies in Drosophila first described these membraneless granules in the oocyte and early embryo as filled with amorphous to fibrillar material mixed with RNA. Genetic studies identified key protein components and specific mRNAs that regulate germ cell‐specific functions. More recently these ultrastructural studies have been complemented by biophysical analysis describing germ granules as phase‐transitioned condensates. In this review, we provide an overview that connects the composition of germ granules with their function in controlling germ cell specification, formation and migration, and illuminate these mysterious condensates as the gatekeepers of the next generation.
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Affiliation(s)
- Tatjana Trcek
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York
| | - Ruth Lehmann
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York
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34
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Whittle CA, Extavour CG. Contrasting patterns of molecular evolution in metazoan germ line genes. BMC Evol Biol 2019; 19:53. [PMID: 30744572 PMCID: PMC6371493 DOI: 10.1186/s12862-019-1363-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/14/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Germ lines are the cell lineages that give rise to the sperm and eggs in animals. The germ lines first arise from primordial germ cells (PGCs) during embryogenesis: these form from either a presumed derived mode of preformed germ plasm (inheritance) or from an ancestral mechanism of inductive cell-cell signalling (induction). Numerous genes involved in germ line specification and development have been identified and functionally studied. However, little is known about the molecular evolutionary dynamics of germ line genes in metazoan model systems. RESULTS Here, we studied the molecular evolution of germ line genes within three metazoan model systems. These include the genus Drosophila (N=34 genes, inheritance), the fellow insect Apis (N=30, induction), and their more distant relative Caenorhabditis (N=23, inheritance). Using multiple species and established phylogenies in each genus, we report that germ line genes exhibited marked variation in the constraint on protein sequence divergence (dN/dS) and codon usage bias (CUB) within each genus. Importantly, we found that de novo lineage-specific inheritance (LSI) genes in Drosophila (osk, pgc) and in Caenorhabditis (pie-1, pgl-1), which are essential to germ plasm functions under the derived inheritance mode, displayed rapid protein sequence divergence relative to the other germ line genes within each respective genus. We show this may reflect the evolution of specialized germ plasm functions and/or low pleiotropy of LSI genes, features not shared with other germ line genes. In addition, we observed that the relative ranking of dN/dS and of CUB between genera were each more strongly correlated between Drosophila and Caenorhabditis, from different phyla, than between Drosophila and its insect relative Apis, suggesting taxonomic differences in how germ line genes have evolved. CONCLUSIONS Taken together, the present results advance our understanding of the evolution of animal germ line genes within three well-known metazoan models. Further, the findings provide insights to the molecular evolution of germ line genes with respect to LSI status, pleiotropy, adaptive evolution as well as PGC-specification mode.
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Affiliation(s)
- Carrie A Whittle
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA.
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA.
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35
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Krishnakumar P, Riemer S, Perera R, Lingner T, Goloborodko A, Khalifa H, Bontems F, Kaufholz F, El-Brolosy MA, Dosch R. Functional equivalence of germ plasm organizers. PLoS Genet 2018; 14:e1007696. [PMID: 30399145 PMCID: PMC6219760 DOI: 10.1371/journal.pgen.1007696] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/16/2018] [Indexed: 11/18/2022] Open
Abstract
The proteins Oskar (Osk) in Drosophila and Bucky ball (Buc) in zebrafish act as germ plasm organizers. Both proteins recapitulate germ plasm activities but seem to be unique to their animal groups. Here, we discover that Osk and Buc show similar activities during germ cell specification. Drosophila Osk induces additional PGCs in zebrafish. Surprisingly, Osk and Buc do not show homologous protein motifs that would explain their related function. Nonetheless, we detect that both proteins contain stretches of intrinsically disordered regions (IDRs), which seem to be involved in protein aggregation. IDRs are known to rapidly change their sequence during evolution, which might obscure biochemical interaction motifs. Indeed, we show that Buc binds to the known Oskar interactors Vasa protein and nanos mRNA indicating conserved biochemical activities. These data provide a molecular framework for two proteins with unrelated sequence but with equivalent function to assemble a conserved core-complex nucleating germ plasm. Multicellular organisms use gametes for their propagation. Gametes are formed from germ cells, which are specified during embryogenesis in some animals by the inheritance of RNP granules known as germ plasm. Transplantation of germ plasm induces extra germ cells, whereas germ plasm ablation leads to the loss of gametes and sterility. Therefore, germ plasm is key for germ cell formation and reproduction. However, the molecular mechanisms of germ cell specification by germ plasm in the vertebrate embryo remain an unsolved question. Proteins, which assemble the germ plasm, are known as germ plasm organizers. Here, we show that the two germ plasm organizers Oskar from the fly and Bucky ball from the fish show similar functions by using a cross species approach. Both are intrinsically disordered proteins, which rapidly changed their sequence during evolution. Moreover, both proteins still interact with conserved components of the germ cell specification pathway. These data might provide a first example of two proteins with the same biological role, but distinct sequence.
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Affiliation(s)
- Pritesh Krishnakumar
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Stephan Riemer
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Roshan Perera
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Thomas Lingner
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Alexander Goloborodko
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Hazem Khalifa
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Franck Bontems
- Laboratory of Metabolism, Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, Switzerland
| | - Felix Kaufholz
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Mohamed A. El-Brolosy
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Roland Dosch
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
- Institute of Human Genetics, University Medical Center, Göttingen, Germany
- * E-mail:
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36
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Ribonuclease activity of MARF1 controls oocyte RNA homeostasis and genome integrity in mice. Proc Natl Acad Sci U S A 2018; 115:11250-11255. [PMID: 30333187 PMCID: PMC6217404 DOI: 10.1073/pnas.1809744115] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Producing normal eggs for fertilization and species propagation requires completion of meiosis and protection of the genome from the ravages of retrotransposons. Mutation of Marf1 (meiosis regulator and mRNA stability factor 1) results in defects in both these key processes in mouse oocytes and thus in infertility. MARF1 was predicted to have ribonuclease activity, but the structural basis for the function of MARF1 and the contribution of its putative ribonuclease domain to the mutant oocyte phenotype was unknown. Therefore, we resolved the crystal structures of key domains of MARF1 and demonstrated by biochemical and mutagenic analyses that the ribonuclease activity of MARF1 controls oocyte meiotic progression and retrotransposon surveillance. The N-terminal NYN domain of MARF1 resembles the nuclease domains of Vpa0982, T4 RNase H, and MCPIP1 and contains four conserved aspartate residues, D178, D215, D246, and D272. The C-terminal LOTUS domain of MARF1 adopts a winged helix-turn-helix fold and binds ssRNA and dsRNA. Purified MARF1 cleaved ssRNAs in vitro, but this cleavage activity was abolished by mutations of conserved aspartates in its NYN domain and truncation of the LOTUS domain. Furthermore, a point mutation in the D272 residue in vivo caused a female-only infertile phenotype in mice, with failure of meiotic resumption and elevation of Line1 and Iap retrotransposon transcripts and DNA double-strand breaks in oocytes. Therefore, the ribonuclease activity of MARF1 controls oocyte meiosis and genome integrity. This activity depends upon conserved aspartic residues in the catalytic NYN domain and the RNA-binding activity of the LOTUS domain.
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LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes. Nat Commun 2018; 9:4031. [PMID: 30279526 PMCID: PMC6168497 DOI: 10.1038/s41467-018-06404-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/01/2018] [Indexed: 12/30/2022] Open
Abstract
Post-transcriptional regulation of gene expression plays an essential role during oocyte maturation. Here we report that Drosophila MARF1 (Meiosis Regulator And mRNA Stability Factor 1), which consists of one RNA-recognition motif and six tandem LOTUS domains with unknown molecular function, is essential for oocyte maturation. When tethered to a reporter mRNA, MARF1 post-transcriptionally silences reporter expression by shortening reporter mRNA poly-A tail length and thereby reducing reporter protein level. This activity is mediated by the MARF1 LOTUS domain, which binds the CCR4-NOT deadenylase complex. MARF1 binds cyclin A mRNA and shortens its poly-A tail to reduce Cyclin A protein level during oocyte maturation. This study identifies MARF1 as a regulator in oocyte maturation and defines the conserved LOTUS domain as a post-transcriptional effector domain that recruits CCR4-NOT deadenylase complex to shorten target mRNA poly-A tails and suppress their translation. The RNA-binding protein MARF1 is required for post-transcriptional regulation of mRNAs during mouse oogenesis. Here, by analyzing a Drosophila MARF1 mutant, the authors show that MARF1 recruits CCR4-NOT deadenylase to shorten the poly-A tails of target mRNAs such as cyclin A and suppress their translation during Drosophila oogenesis.
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38
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Durdevic Z, Pillai RS, Ephrussi A. Transposon silencing in the Drosophila female germline is essential for genome stability in progeny embryos. Life Sci Alliance 2018; 1:e201800179. [PMID: 30456388 PMCID: PMC6238532 DOI: 10.26508/lsa.201800179] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 12/21/2022] Open
Abstract
The Piwi-interacting RNA pathway functions in transposon control in the germline of metazoans. The conserved RNA helicase Vasa is an essential Piwi-interacting RNA pathway component, but has additional important developmental functions. Here, we address the importance of Vasa-dependent transposon control in the Drosophila female germline and early embryos. We find that transient loss of vasa expression during early oogenesis leads to transposon up-regulation in supporting nurse cells of the fly egg-chamber. We show that elevated transposon levels have dramatic consequences, as de-repressed transposons accumulate in the oocyte where they cause DNA damage. We find that suppression of Chk2-mediated DNA damage signaling in vasa mutant females restores oogenesis and egg production. Damaged DNA and up-regulated transposons are transmitted from the mother to the embryos, which sustain severe nuclear defects and arrest development. Our findings reveal that the Vasa-dependent protection against selfish genetic elements in the nuage of nurse cell is essential to prevent DNA damage-induced arrest of embryonic development.
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Affiliation(s)
- Zeljko Durdevic
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ramesh S Pillai
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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39
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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] [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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40
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TDRD5 binds piRNA precursors and selectively enhances pachytene piRNA processing in mice. Nat Commun 2018; 9:127. [PMID: 29317670 PMCID: PMC5760656 DOI: 10.1038/s41467-017-02622-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/11/2017] [Indexed: 11/08/2022] Open
Abstract
Pachytene piRNAs are the most abundant piRNAs in mammalian adult testes. They are generated from long precursor transcripts by the primary piRNA biogenesis pathway but the factors involved in pachytene piRNA precursors processing are poorly understood. Here we show that the Tudor domain-containing 5 (TDRD5) protein is essential for pachytene piRNA biogenesis in mice. Conditional inactivation of TDRD5 in mouse postnatal germ cells reveals that TDRD5 selectively regulates the production of pachytene piRNAs from abundant piRNA-producing precursors, with little effect on low-abundant piRNAs. Unexpectedly, TDRD5 is not required for the 5′ end processing of the precursors, but is crucial for promoting production of piRNAs from the other regions of the transcript. Furthermore, we show that TDRD5 is an RNA-binding protein directly associating with piRNA precursors. These observations establish TDRD5 as a piRNA biogenesis factor and reveal two genetically separable steps at the start of pachytene piRNA processing. Pachytene piRNAs are abundant piRNAs in mammalian adult testes but their biogenesis pathway is not fully understood. Here, the authors identify TDRD5 as a piRNA biogenesis factor in mice, showing that it binds piRNA precursors and promotes pachytene piRNA production from specific transcript regions.
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41
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Retrotransposons Mimic Germ Plasm Determinants to Promote Transgenerational Inheritance. Curr Biol 2017; 27:3010-3016.e3. [PMID: 28966088 DOI: 10.1016/j.cub.2017.08.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 07/14/2017] [Accepted: 08/15/2017] [Indexed: 11/21/2022]
Abstract
Retrotransposons are a pervasive class of mobile elements present in the genomes of virtually all forms of life [1, 2]. In metazoans, these are preferentially active in the germline, which, in turn, mounts defenses that restrain their activity [3, 4]. Here we report that certain classes of retrotransposons ensure transgenerational inheritance by invading presumptive germ cells before they are formed. Using sensitized Drosophila and zebrafish models, we found that diverse classes of retrotransposons migrate to the germ plasm, a specialized region of the oocyte that prefigures germ cells and specifies the germline of descendants in the fertilized egg. In Drosophila, we found evidence for a "stowaway" model, whereby Tahre retroelements traffic to the germ plasm by mimicking oskar RNAs and engaging the Staufen-dependent active transport machinery. Consistent with this, germ plasm determinants attracted retroelement RNAs even when these components were ectopically positioned in bipolar oocytes. Likewise, vertebrate retrotransposons similarly migrated to the germ plasm in zebrafish oocytes. Together, these results suggest that germ plasm targeting represents a fitness strategy adopted by some retrotransposons to ensure transgenerational propagation.
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42
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Huang X, Fejes Tóth K, Aravin AA. piRNA Biogenesis in Drosophila melanogaster. Trends Genet 2017; 33:882-894. [PMID: 28964526 DOI: 10.1016/j.tig.2017.09.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a conserved defense system that protects the genome integrity of the animal germline from deleterious transposable elements. Targets of silencing are recognized by small noncoding piRNAs that are processed from long precursor molecules. Although piRNAs and other classes of small noncoding RNAs, such as miRNAs and small interfering (si)RNAs, interact with members of the same family of Argonaute (Ago) proteins and their function in target repression is similar, the biogenesis of piRNAs differs from those of the other two small RNAs. Recently, many aspects of piRNA biogenesis have been revealed in Drosophila melanogaster. In this review, we elaborate on piRNA biogenesis in Drosophila somatic and germline cells. We focus on the mechanisms by which piRNA precursor transcription is regulated and highlight recent work that has advanced our understanding of piRNA precursor processing to mature piRNAs. We finish by discussing current models to the still unresolved question of how piRNA precursors are selected and channeled into the processing machinery.
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Affiliation(s)
- Xiawei Huang
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
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43
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Bilinski SM, Jaglarz MK, Tworzydlo W. The Pole (Germ) Plasm in Insect Oocytes. Results Probl Cell Differ 2017; 63:103-126. [PMID: 28779315 DOI: 10.1007/978-3-319-60855-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Animal germline cells are specified either through zygotic induction or cytoplasmic inheritance. Zygotic induction takes place in mid- or late embryogenesis and requires cell-to-cell signaling leading to the acquisition of germline fate de novo. In contrast, cytoplasmic inheritance involves formation of a specific, asymmetrically localized oocyte region, termed the germ (pole) plasm. This region contains maternally provided germline determinants (mRNAs, proteins) that are capable of inducing germline fate in a subset of embryonic cells. Recent data indicate that among insects, the zygotic induction represents an ancestral condition, while the cytoplasmic inheritance evolved at the base of Holometabola or in the last common ancestor of Holometabola and its sister taxon, Paraneoptera.In this chapter, we first describe subsequent stages of morphogenesis of the pole plasm and polar granules in the model organism, Drosophila melanogaster. Then, we present an overview of morphology and cytoarchitecture of the pole plasm in various holometabolan and paraneopteran insect species. Finally, we focus on phylogenetic hypotheses explaining the known distribution of two different strategies of germline specification among insects.
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Affiliation(s)
- Szczepan M Bilinski
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland.
| | - Mariusz K Jaglarz
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland
| | - Waclaw Tworzydlo
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland
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44
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Abstract
Asymmetric localization of mRNAs is a widespread gene regulatory mechanism that is crucial for many cellular processes. The localization of a transcript involves multiple steps and requires several protein factors to mediate transport, anchoring and translational repression of the mRNA. Specific recognition of the localizing transcript is a key step that depends on linear or structured localization signals, which are bound by RNA-binding proteins. Genetic studies have identified many components involved in mRNA localization. However, mechanistic aspects of the pathway are still poorly understood. Here we provide an overview of structural studies that contributed to our understanding of the mechanisms underlying mRNA localization, highlighting open questions and future challenges.
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Affiliation(s)
| | - Fulvia Bono
- a Max Planck Institute for Developmental Biology , Tübingen , Germany
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45
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Kulkarni A, Extavour CG. Convergent evolution of germ granule nucleators: A hypothesis. Stem Cell Res 2017; 24:188-194. [PMID: 28801028 DOI: 10.1016/j.scr.2017.07.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/18/2017] [Accepted: 07/15/2017] [Indexed: 11/26/2022] Open
Abstract
Germ cells have been considered "the ultimate stem cell" because they alone, during normal development of sexually reproducing organisms, are able to give rise to all organismal cell types. Morphological descriptions of a specialized cytoplasm termed 'germ plasm' and associated electron dense ribonucleoprotein (RNP) structures called 'germ granules' within germ cells date back as early as the 1800s. Both germ plasm and germ granules are implicated in germ line specification across metazoans. However, at a molecular level, little is currently understood about the molecular mechanisms that assemble these entities in germ cells. The discovery that in some animals, the gene products of a small number of lineage-specific genes initiate the assembly (also termed nucleation) of germ granules and/or germ plasm is the first step towards facilitating a better understanding of these complex biological processes. Here, we draw on research spanning over 100years that supports the hypothesis that these nucleator genes may have evolved convergently, allowing them to perform analogous roles across animal lineages.
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Affiliation(s)
- Arpita Kulkarni
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
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46
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Jeske M, Müller CW, Ephrussi A. The LOTUS domain is a conserved DEAD-box RNA helicase regulator essential for the recruitment of Vasa to the germ plasm and nuage. Genes Dev 2017; 31:939-952. [PMID: 28536148 PMCID: PMC5458760 DOI: 10.1101/gad.297051.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/08/2017] [Indexed: 12/15/2022]
Abstract
DEAD-box RNA helicases play important roles in a wide range of metabolic processes. Regulatory proteins can stimulate or block the activity of DEAD-box helicases. Here, we show that LOTUS (Limkain, Oskar, and Tudor containing proteins 5 and 7) domains present in the germline proteins Oskar, TDRD5 (Tudor domain-containing 5), and TDRD7 bind and stimulate the germline-specific DEAD-box RNA helicase Vasa. Our crystal structure of the LOTUS domain of Oskar in complex with the C-terminal RecA-like domain of Vasa reveals that the LOTUS domain occupies a surface on a DEAD-box helicase not implicated previously in the regulation of the enzyme's activity. We show that, in vivo, the localization of Drosophila Vasa to the nuage and germ plasm depends on its interaction with LOTUS domain proteins. The binding and stimulation of Vasa DEAD-box helicases by LOTUS domains are widely conserved.
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Affiliation(s)
- Mandy Jeske
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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47
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Mitochondrial matters: Mitochondrial bottlenecks, self-assembling structures, and entrapment in the female germline. Stem Cell Res 2017; 21:178-186. [PMID: 28336253 DOI: 10.1016/j.scr.2017.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/22/2016] [Accepted: 03/10/2017] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial replacement therapy, a procedure to generate embryos with the nuclear genome of a donor mother and the healthy mitochondria of a recipient egg, has recently emerged as a promising strategy to prevent transmission of devastating mitochondrial DNA diseases and infertility. The procedure may produce an embryo that is free of diseased mitochondria. A recent study addresses important fundamental questions about the mechanisms underlying maternal inheritance and translational questions regarding the transgenerational effectiveness of this promising therapeutic strategy. This review considers recent advances in our understanding of maternal inheritance of mitochondria, implications for fertility and mitochondrial disease, and potential roles for the Balbiani body, an ancient oocyte structure, in mitochondrial selection in oocytes, with emphasis on therapies to remedy mitochondrial disorders.
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48
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Abstract
Acquisition of oocyte polarity involves complex translocation and aggregation of intracellular organelles, RNAs, and proteins, along with strict posttranscriptional regulation. While much is still unknown regarding the formation of the animal-vegetal axis, an early marker of polarity, animal models have contributed to our understanding of these early processes controlling normal oogenesis and embryo development. In recent years, it has become clear that proteins with self-assembling properties are involved in assembling discrete subcellular compartments or domains underlying subcellular asymmetries in the early mitotic and meiotic cells of the female germline. These include asymmetries in duplication of the centrioles and formation of centrosomes and assembly of the organelle and RNA-rich Balbiani body, which plays a critical role in oocyte polarity. Notably, at specific stages of germline development, these transient structures in oocytes are temporally coincident and align with asymmetries in the position and arrangement of nuclear components, such as the nuclear pore and the chromosomal bouquet and the centrioles and cytoskeleton in the cytoplasm. Formation of these critical, transient structures and arrangements involves microtubule pathways, intrinsically disordered proteins (proteins with domains that tend to be fluid or lack a rigid ordered three-dimensional structure ranging from random coils, globular domains, to completely unstructured proteins), and translational repressors and activators. This review aims to examine recent literature and key players in oocyte polarity.
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Affiliation(s)
- Mara Clapp
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
| | - Florence L Marlow
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA.
- Department of Neuroscience, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA.
- Department of Cell, Developmental and Regenerative Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029-6574, USA.
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49
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Goldman CH, Gonsalvez GB. The Role of Microtubule Motors in mRNA Localization and Patterning Within the Drosophila Oocyte. Results Probl Cell Differ 2017; 63:149-168. [PMID: 28779317 DOI: 10.1007/978-3-319-60855-6_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Messenger RNA (mRNA) localization is a powerful and prevalent mechanism of post-transcriptional gene regulation, enabling the cell to produce protein at the exact location at which it is needed. The phenomenon of mRNA localization has been observed in many types of cells in organisms ranging from yeast to man. Thus, the process appears to be widespread and highly conserved. Several model systems have been used to understand the mechanism by which mRNAs are localized. One such model, and the focus of this chapter, is the egg chamber of the female Drosophila melanogaster. The polarity of the developing Drosophila oocyte and resulting embryo relies on the specific localization of three critical mRNAs: gurken, bicoid, and oskar. If these mRNAs are not localized during oogenesis, the resulting progeny will not survive. The study of these mRNAs has served as a model for understanding the general mechanisms by which mRNAs are sorted. In this chapter, we will discuss how the localization of these mRNAs enables polarity establishment. We will also discuss the role of motor proteins in the localization pathway. Finally, we will consider potential mechanisms by which mRNAs can be anchored at their site of localization. It is likely that the lessons learned using the Drosophila oocyte model system will be applicable to mRNAs that are localized in other organisms as well.
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Affiliation(s)
- Chandler H Goldman
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd., CB2917, Augusta, GA, 30912, USA
| | - Graydon B Gonsalvez
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd., CB2917, Augusta, GA, 30912, USA.
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50
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Sampath K, Ephrussi A. CncRNAs: RNAs with both coding and non-coding roles in development. Development 2016; 143:1234-41. [PMID: 27095489 DOI: 10.1242/dev.133298] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNAs are known to regulate diverse biological processes, either as protein-encoding molecules or as non-coding RNAs. However, a third class that comprises RNAs endowed with both protein coding and non-coding functions has recently emerged. Such bi-functional 'coding and non-coding RNAs' (cncRNAs) have been shown to play important roles in distinct developmental processes in plants and animals. Here, we discuss key examples of cncRNAs and review their roles, regulation and mechanisms of action during development.
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Affiliation(s)
- Karuna Sampath
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AJ, UK
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
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