1
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Chen R, Stainier W, Dufourt J, Lagha M, Lehmann R. Direct observation of translational activation by a ribonucleoprotein granule. Nat Cell Biol 2024:10.1038/s41556-024-01452-5. [PMID: 38965420 DOI: 10.1038/s41556-024-01452-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 05/30/2024] [Indexed: 07/06/2024]
Abstract
Biomolecular condensates organize biochemical processes at the subcellular level and can provide spatiotemporal regulation within a cell. Among these, ribonucleoprotein (RNP) granules are storage hubs for translationally repressed mRNA. Whether RNP granules can also activate translation and how this could be achieved remains unclear. Here, using single-molecule imaging, we demonstrate that the germ cell-determining RNP granules in Drosophila embryos are sites for active translation of nanos mRNA. Nanos translation occurs preferentially at the germ granule surface with the 3' UTR buried within the granule. Smaug, a cytosolic RNA-binding protein, represses nanos translation, which is relieved when Smaug is sequestered to the germ granule by the scaffold protein Oskar. Together, our findings uncover a molecular process by which RNP granules achieve localized protein synthesis through the compartmentalized loss of translational repression.
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Affiliation(s)
- Ruoyu Chen
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Vilcek Institute of Graduate Studies, NYU School of Medicine, New York, NY, USA
| | - William Stainier
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Immunobiology Laboratory, The Francis Crick Institute, London, UK
| | - Jeremy Dufourt
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, Montpellier, France
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, Montpellier, France
| | - Mounia Lagha
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, Montpellier, France
| | - Ruth Lehmann
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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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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3
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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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4
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Kubíková J, Ubartaitė G, Metz J, Jeske M. Structural basis for binding of Drosophila Smaug to the GPCR Smoothened and to the germline inducer Oskar. Proc Natl Acad Sci U S A 2023; 120:e2304385120. [PMID: 37523566 PMCID: PMC10410706 DOI: 10.1073/pnas.2304385120] [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: 03/27/2023] [Accepted: 06/28/2023] [Indexed: 08/02/2023] Open
Abstract
Drosophila Smaug and its orthologs comprise a family of mRNA repressor proteins that exhibit various functions during animal development. Smaug proteins contain a characteristic RNA-binding sterile-α motif (SAM) domain and a conserved but uncharacterized N-terminal domain (NTD). Here, we resolved the crystal structure of the NTD of the human SAM domain-containing protein 4A (SAMD4A, a.k.a. Smaug1) to 1.6 Å resolution, which revealed its composition of a homodimerization D subdomain and a subdomain with similarity to a pseudo-HEAT-repeat analogous topology (PHAT) domain. Furthermore, we show that Drosophila Smaug directly interacts with the Drosophila germline inducer Oskar and with the Hedgehog signaling transducer Smoothened through its NTD. We determined the crystal structure of the NTD of Smaug in complex with a Smoothened α-helical peptide to 2.0 Å resolution. The peptide binds within a groove that is formed by both the D and PHAT subdomains. Structural modeling supported by experimental data suggested that an α-helix within the disordered region of Oskar binds to the NTD of Smaug in a mode similar to Smoothened. Together, our data uncover the NTD of Smaug as a peptide-binding domain.
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Affiliation(s)
- Jana Kubíková
- Biochemistry Center, Heidelberg University, Heidelberg69120, Germany
| | | | - Jutta Metz
- Biochemistry Center, Heidelberg University, Heidelberg69120, Germany
| | - Mandy Jeske
- Biochemistry Center, Heidelberg University, Heidelberg69120, Germany
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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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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. Evolutionary changes in germ granule mRNA content are driven by multiple mechanisms in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529147. [PMID: 36865184 PMCID: PMC9980053 DOI: 10.1101/2023.02.21.529147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The co-packaging of mRNAs into biomolecular condensates called germ granules is a conserved strategy to post-transcriptionally regulate mRNAs that function in germline development and maintenance. In D. melanogaster, mRNAs accumulate in germ granules by forming homotypic clusters, aggregates that contain multiple transcripts from a specific gene. Nucleated by Oskar (Osk), homotypic clusters in D. melanogaster are generated through a stochastic seeding and self-recruitment process that requires the 3' 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. Thus, we hypothesized that evolutionary changes in the 3' UTR influences germ granule development. To test our hypothesis, we investigated the homotypic clustering of nos and polar granule component (pgc) in four Drosophila species and concluded that homotypic clustering is a conserved developmental process used to enrich germ granule mRNAs. Additionally, we discovered that the number of transcripts found in nos and/or pgc clusters could vary significantly among species. By integrating biological data with computational modeling, we determined that multiple mechanisms underlie naturally occurring germ granule diversity, including changes in nos, pgc, osk levels, and/or homotypic clustering efficacy. Finally, we found that the nos 3' UTR from different species can alter the efficacy of nos homotypic clustering, resulting in germ granules with reduced nos accumulation. Our findings highlight the impact that evolution has on the development of germ granules and may provide insight into processes that modify the content of other classes of biomolecular condensates.
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Affiliation(s)
- Dominique A. Doyle
- School of Integrative Science and Technology, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
| | - Florencia N. Burian
- School of Integrative Science and Technology, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
| | - Benjamin Aharoni
- School of Integrative Science and Technology, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
| | - Annabelle J. Klinder
- School of Integrative Science and Technology, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
| | - Melissa M. Menzel
- School of Integrative Science and Technology, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
| | - Gerard Carlo C. Nifras
- School of Integrative Science and Technology, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
| | - Ahad L. Shabazz-Henry
- School of Integrative Science and Technology, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
| | - Bianca Ulrich Palma
- School of Integrative Science and Technology, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
| | - Gisselle A. Hidalgo
- School of Integrative Science and Technology, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
| | - Christopher J. Sottolano
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ 08103, USA
| | - Bianca M. Ortega
- School of Integrative Science and Technology, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
| | - Matthew G. Niepielko
- School of Integrative Science and Technology, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
- Department of Biological Sciences, Kean University, 1000 Morris Ave., Union, NJ 07083, USA
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9
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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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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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Valentino M, Ortega BM, Ulrich B, Doyle DA, Farnum ED, Joiner DA, Gavis ER, Niepielko MG. Computational modeling offers new insight into Drosophila germ granule development. Biophys J 2022; 121:1465-1482. [PMID: 35288123 PMCID: PMC9072583 DOI: 10.1016/j.bpj.2022.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/04/2022] [Accepted: 03/09/2022] [Indexed: 11/02/2022] Open
Abstract
The packaging of specific mRNAs into ribonucleoprotein granules called germ granules is required for germline proliferation and maintenance. During Drosophila germ granule development, mRNAs such as nanos (nos) and polar granule component (pgc) localize to germ granules through a stochastic seeding and self-recruitment process that generates homotypic clusters: aggregates containing multiple copies of a specific transcript. Germ granules vary in mRNA composition with respect to the different transcripts that they contain and their quantity. However, what influences germ granule mRNA composition during development is unclear. To gain insight into how germ granule mRNA heterogeneity arises, we created a computational model that simulates granule development. Although the model includes known mechanisms that were converted into mathematical representations, additional unreported mechanisms proved to be essential for modeling germ granule formation. The model was validated by predicting defects caused by changes in mRNA and protein abundance. Broader application of the model was demonstrated by quantifying nos and pgc localization efficacies and the contribution that an element within the nos 3' untranslated region has on clustering. For the first time, a mathematical representation of Drosophila germ granule formation is described, offering quantitative insight into how mRNA compositions arise while providing a new tool for guiding future studies.
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12
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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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13
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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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14
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Ren F, Miao R, Xiao R, Mei J. m 6A reader Igf2bp3 enables germ plasm assembly by m 6A-dependent regulation of gene expression in zebrafish. Sci Bull (Beijing) 2021; 66:1119-1128. [PMID: 36654345 DOI: 10.1016/j.scib.2021.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/13/2020] [Accepted: 10/27/2020] [Indexed: 01/20/2023]
Abstract
Bucky ball (Buc) is involved in germ plasm (GP) assembly during early zebrafish development by regulating GP mRNA expression via an unknown mechanism. The present study demonstrates that an m6A reader Igf2bp3 interacts and colocalizes with Buc in the GP. Similar to the loss of Buc, the genetic deletion of maternal igf2bp3 in zebrafish leads to abnormal GP assembly and insufficient germ cell specification, which can be partially restored by the injection of igf2bp3 mRNA. Igf2bp3 binds to m6A-modified GP-organizer and GP mRNAs in an m6A-dependent manner and prevents their degradation. These findings indicate that the functions of Igf2bp3, a direct effector protein of Buc, in GP mRNA expression and GP assembly involve m6A-dependent regulation; these results emphasize a critical role of m6A modification in the process of GP assembly.
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Affiliation(s)
- Fan Ren
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Ran Miao
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Rui Xiao
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan 430071, China; Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China.
| | - Jie Mei
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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15
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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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16
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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: 13] [Impact Index Per Article: 4.3] [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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17
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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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18
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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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19
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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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20
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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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21
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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: 12] [Impact Index Per Article: 3.0] [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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22
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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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23
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Jones R, Lessoued S, Meier K, Devignot S, Barata-García S, Mate M, Bragagnolo G, Weber F, Rosenthal M, Reguera J. Structure and function of the Toscana virus cap-snatching endonuclease. Nucleic Acids Res 2020; 47:10914-10930. [PMID: 31584100 PMCID: PMC6847833 DOI: 10.1093/nar/gkz838] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 09/14/2019] [Accepted: 10/01/2019] [Indexed: 12/03/2022] Open
Abstract
Toscana virus (TOSV) is an arthropod-borne human pathogen responsible for seasonal outbreaks of fever and meningoencephalitis in the Mediterranean basin. TOSV is a segmented negative-strand RNA virus (sNSV) that belongs to the genus phlebovirus (family Phenuiviridae, order Bunyavirales), encompassing other important human pathogens such as Rift Valley fever virus (RVFV). Here, we carried out a structural and functional characterization of the TOSV cap-snatching endonuclease, an N terminal domain of the viral polymerase (L protein) that provides capped 3′OH primers for transcription. We report TOSV endonuclease crystal structures in the apo form, in complex with a di-ketoacid inhibitor (DPBA) and in an intermediate state of inhibitor release, showing details on substrate binding and active site dynamics. The structure reveals substantial folding rearrangements absent in previously reported cap-snatching endonucleases. These include the relocation of the N terminus and the appearance of new structural motifs important for transcription and replication. The enzyme shows high activity rates comparable to other His+ cap-snatching endonucleases. Moreover, the activity is dependent on conserved residues involved in metal ion and substrate binding. Altogether, these results bring new light on the structure and function of cap-snatching endonucleases and pave the way for the development of specific and broad-spectrum antivirals.
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Affiliation(s)
- Rhian Jones
- Aix-Marseille Université, CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Sana Lessoued
- Aix-Marseille Université, CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Kristina Meier
- Bernhard Nocht Institute for Tropical Medicine, Department of Virology, D-20359 Hamburg, Germany
| | - Stéphanie Devignot
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, D-35392 Giessen, Germany
| | | | - Maria Mate
- Aix-Marseille Université, CNRS, AFMB UMR 7257, 13288 Marseille, France
| | | | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, D-35392 Giessen, Germany
| | - Maria Rosenthal
- Bernhard Nocht Institute for Tropical Medicine, Department of Virology, D-20359 Hamburg, Germany
| | - Juan Reguera
- Aix-Marseille Université, CNRS, AFMB UMR 7257, 13288 Marseille, France.,INSERM, AFMB UMR7257,13288 Marseille, France
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24
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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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25
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Lee CYS, Putnam A, Lu T, He S, Ouyang JPT, Seydoux G. Recruitment of mRNAs to P granules by condensation with intrinsically-disordered proteins. eLife 2020; 9:e52896. [PMID: 31975687 PMCID: PMC7007223 DOI: 10.7554/elife.52896] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/23/2020] [Indexed: 12/30/2022] Open
Abstract
RNA granules are protein/RNA condensates. How specific mRNAs are recruited to cytoplasmic RNA granules is not known. Here, we characterize the transcriptome and assembly of P granules, RNA granules in the C. elegans germ plasm. We find that P granules recruit mRNAs by condensation with the disordered protein MEG-3. MEG-3 traps mRNAs into non-dynamic condensates in vitro and binds to ~500 mRNAs in vivo in a sequence-independent manner that favors embryonic mRNAs with low ribosome coverage. Translational stress causes additional mRNAs to localize to P granules and translational activation correlates with P granule exit for two mRNAs coding for germ cell fate regulators. Localization to P granules is not required for translational repression but is required to enrich mRNAs in the germ lineage for robust germline development. Our observations reveal similarities between P granules and stress granules and identify intrinsically-disordered proteins as drivers of RNA condensation during P granule assembly.
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Affiliation(s)
- Chih-Yung S Lee
- HHMI and Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreUnited States
| | - Andrea Putnam
- HHMI and Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreUnited States
| | - Tu Lu
- HHMI and Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreUnited States
| | - ShuaiXin He
- HHMI and Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreUnited States
- Department of Biophysics and Biophysical ChemistryJohns Hopkins University School of MedicineBaltimoreUnited States
| | - John Paul T Ouyang
- HHMI and Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreUnited States
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreUnited States
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26
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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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27
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Jariyapong P, Pudgerd A, Cheloh N, Hirono I, Kondo H, Vanichviriyakit R, Weerachatyanukul W, Chotwiwatthanakun C. Hematopoietic tissue of Macrobrachium rosenbergii plays dual roles as a source of hemocyte hematopoiesis and as a defensive mechanism against Macrobrachium rosenbergii nodavirus infection. FISH & SHELLFISH IMMUNOLOGY 2019; 86:756-763. [PMID: 30553890 DOI: 10.1016/j.fsi.2018.12.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/03/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
White tail disease caused by Macrobrachium rosenbergii nodavirus (MrNV) infection takes place only in nauplii, not adults, of M. rosenbergii prawn. Hemocyte homeostasis and immune-related functions derived from the hematopoietic tissue (Hpt) in adult prawn are presumed to play roles in resisting viral infection. To elucidate the role of the Hpt cell response to MrNV, a comparative transcriptome analysis was performed with MrNV-infected prawn at various time intervals. The results showed that there were 462 unigenes that were differentially expressed between mock and infected samples. BlastX sequence analysis revealed that two proteins, crustacean hematopoietic factor (CHF) and cell growth-regulating zinc finger protein (Lyar), are involved in hemocyte hematopoiesis and are up-regulated during MrNV infection. In fact, genes involved in cell growth regulation and immunity were highly expressed at 6 h and decreased within 24 h post-infection. Localization studies in the Hpt tissue revealed the presence of anti-lipopolysaccharide factor (ALF) and CHF mRNAs in Hpt cells. Considering these findings, we concluded that resistance to MrNV infection in adult prawn is due to an increase in humoral immune factors and the acceleration of hemocyte homeostasis by the dual roles of the Hpt organ in M. rosenbergii.
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Affiliation(s)
- Pitchanee Jariyapong
- School of Medicine, Walailak University, Thasala District, Nakhonsrithammarat, 80161, Thailand; Research Center of Excellence on Shrimp, Walailak University, Thasala District, Nakhonsrithammarat, 80161, Thailand
| | - Arnon Pudgerd
- Division of Anatomy, School of Medical Science, University of Phayao, Muang, Phayao, 56000, Thailand; Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Nifareesa Cheloh
- Faculty of Agriculture, Princess of Naradhiwas University, Mueang Narathiwat District, Narathiwat, 96000, Thailand
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato, Tokyo, 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato, Tokyo, 108-8477, Japan
| | - Rapeepun Vanichviriyakit
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand; Department of Anatomy, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Wattana Weerachatyanukul
- Department of Anatomy, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Charoonroj Chotwiwatthanakun
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand; Nakhonsawan Campus, Mahidol University, Nakhonsawan, 60130, Thailand.
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28
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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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29
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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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30
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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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31
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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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32
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Kulandaisamy A, Srivastava A, Kumar P, Nagarajan R, Priya SB, Gromiha MM. Identification and Analysis of Key Residues in Protein-RNA Complexes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1436-1444. [PMID: 29993582 DOI: 10.1109/tcbb.2018.2834387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Protein-RNA complexes play important roles in various biological processes. The functions of protein-RNA complexes are dictated by their interactions, binding, stability, and affinity. In this work, we have identified the key residues (KRs), which are involved in both stability and binding. We found that 42 percent of considered proteins share common binding and stabilizing residues, whereas these residues are distinct in 58 percent of the proteins. Overall, 5 percent of stabilizing and 3 percent of binding residues serve as key residues. These residues are enriched with the combination of polar, charged, aliphatic, and aromatic residues. Analysis on subclasses of protein-RNA complexes based on protein structural class, function and RNA type showed that regulatory proteins, and complexes with single stranded RNA and rRNA have appreciable number of key residues. Specifically, Arg, Tyr, and Thr are preferred in most of the subclasses of protein-RNA complexes. In addition, residues with similar chemical behavior have different preferences to be KRs, such that Arg, Tyr, Val, and Thr are preferred over Lys, Trp, Ile, and Ser, respectively. Atomic level contacts revealed that charged and polar-nonpolar contacts are dominant in enzymes, polar in structural, and nonpolar in regulatory proteins. On the other hand, polar-nonpolar contacts are enriched in all these classes of protein-RNA complexes. Further, the influence of sequence and structural features such as conservation score, surrounding hydrophobicity, solvent accessibility, secondary structure, and long-range order in key residues are also discussed. We envisage that the present study provides insights to understand the structural and functional aspects of protein-RNA complexes.
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33
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Stochastic Seeding Coupled with mRNA Self-Recruitment Generates Heterogeneous Drosophila Germ Granules. Curr Biol 2018; 28:1872-1881.e3. [PMID: 29861136 DOI: 10.1016/j.cub.2018.04.037] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/27/2018] [Accepted: 04/12/2018] [Indexed: 11/22/2022]
Abstract
The formation of ribonucleoprotein assemblies called germ granules is a conserved feature of germline development. In Drosophila, germ granules form at the posterior of the oocyte in a specialized cytoplasm called the germ plasm, which specifies germline fate during embryogenesis. mRNAs, including nanos (nos) and polar granule component (pgc), that function in germline development are localized to the germ plasm through their incorporation into germ granules, which deliver them to the primordial germ cells. Germ granules are nucleated by Oskar (Osk) protein and contain varying combinations and quantities of their constituent mRNAs, which are organized as spatially distinct, multi-copy homotypic clusters. The process that gives rise to such heterogeneous yet organized granules remains unknown. Here, we show that individual nos and pgc transcripts can populate the same nascent granule, and these first transcripts then act as seeds, recruiting additional like transcripts to form homotypic clusters. Within a granule, homotypic clusters grow independently of each other but depend on the simultaneous acquisition of additional Osk. Although granules can contain multiple clusters of a particular mRNA, granule mRNA content is dominated by cluster size. These results suggest that the accumulation of mRNAs in the germ plasm is controlled by the mRNAs themselves through their ability to form homotypic clusters; thus, RNA self-association drives germ granule mRNA localization. We propose that a stochastic seeding and self-recruitment mechanism enables granules to simultaneously incorporate many different mRNAs while ensuring that each becomes enriched to a functional threshold.
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34
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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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35
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Olczak A, Cianci M. The signal-to-noise ratio in SAD experiments. CRYSTALLOGR REV 2017. [DOI: 10.1080/0889311x.2017.1386182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Andrzej Olczak
- Institute of General and Ecological Chemistry, Lodz University of Technology, Lodz, Poland
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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36
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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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37
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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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38
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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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39
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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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40
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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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41
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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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42
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Determinants of affinity and specificity in RNA-binding proteins. Curr Opin Struct Biol 2016; 38:83-91. [PMID: 27315040 DOI: 10.1016/j.sbi.2016.05.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 12/21/2022]
Abstract
Emerging data suggest that the mechanisms by which RNA-binding proteins (RBPs) interact with RNA and the rules governing specificity might be substantially more complex than those underlying their DNA-binding counterparts. Even our knowledge of what constitutes the RNA-bound proteome is contentious; recent studies suggest that 10-30% of RBPs contain no known RNA-binding domain. Adding to this situation is a growing disconnect between the avalanche of identified interactions between proteins and long noncoding RNAs and the absence of biophysical data on these interactions. RNA-protein interactions are also at the centre of what might emerge as one of the biggest shifts in thinking about cell and molecular biology this century, following from recent reports of ribonucleoprotein complexes that drive reversible membrane-free phase separation events within the cell. Unexpectedly, low-complexity motifs are important in the formation of these structures. Here we briefly survey recent advances in our understanding of the specificity of RBPs.
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43
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Abstract
Germ granules are the hallmark of all germ cells. These membrane-less, electron-dense structures were first observed over 100 years ago. Today, their role in regulating and processing transcripts critical for the establishment, maintenance, and protection of germ cells is well established, and pathways outlining the biochemical mechanisms and physical properties associated with their biogenesis are emerging.
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Affiliation(s)
- Ruth Lehmann
- Howard Hughes Medical Institute (HHMI), Department of Cell Biology, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, USA.
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44
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Quan H, Lynch JA. The evolution of insect germline specification strategies. CURRENT OPINION IN INSECT SCIENCE 2016; 13:99-105. [PMID: 27088076 PMCID: PMC4827259 DOI: 10.1016/j.cois.2016.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The establishment of the germline is essential for sexually reproducing organisms. In animals, there are two major strategies to specify the germline: maternal provision and zygotic induction. The molecular basis of the maternal provision mode has been well characterized in several model organisms (fly, frog, fish, and nematode), while that of the zygotic induction mode has mainly been studied in mammalian models such as the mouse. Shifts in germline determination modes occur unexpectedly frequently and many such shifts have occurred several times among insects. Given their general tractability and rapidly increasing genomic and genetic tools applicable to many species, the insects present a uniquely powerful model system for understanding major transitions in reproductive strategies, and developmental processes in general.
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Affiliation(s)
- Honghu Quan
- Department of Biological Sciences, University of Illinois at Chicago, United States
| | - Jeremy A Lynch
- Department of Biological Sciences, University of Illinois at Chicago, United States.
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45
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Abstract
Primordial germ cells are usually made early in the development of an organism. These are the mother of all stem cells that are necessary for propagation of the species, yet use highly diverse mechanisms between organisms. How they are specified, and when and where they form, are central to developmental biology. Using diverse organisms to study this development is illuminating for understanding the mechanics these cells use in this essential function and for identifying the breadth of evolutionary changes that have occurred between species. This essay emphasizes how echinoderms may contribute to the patchwork quilt of our understanding of germ line formation during embryogenesis.
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Affiliation(s)
- Gary M Wessel
- Department of Molecular and Cellular Biology, Brown University, Providence, Rhode Island, USA.
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