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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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2
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Pieplow C, Wessel G. Functional annotation of a hugely expanded nanos repertoire in Lytechinus variegatus, the green sea urchin. Mol Reprod Dev 2023; 90:310-322. [PMID: 37039283 PMCID: PMC10225336 DOI: 10.1002/mrd.23684] [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: 11/21/2022] [Revised: 02/17/2023] [Accepted: 03/18/2023] [Indexed: 04/12/2023]
Abstract
Nanos genes encode essential RNA-binding proteins involved in germline determination and germline stem cell maintenance. When examining diverse classes of echinoderms, typically three, sometimes four, nanos genes are present. In this analysis, we identify and annotate nine nanos orthologs in the green sea urchin, Lytechinus variegatus (Lv). All nine genes are transcribed and grouped into three distinct classes. Class one includes the germline Nanos, with one member: Nanos2. Class two includes Nanos3-like genes, with significant sequence similarity to Nanos3 in the purple sea urchin, Strongylocentrotus purpuratus (Sp), but with wildly variable expression patterns. The third class includes several previously undescribed nanos zinc-finger genes that may be the result of duplications of Nanos2. All nine nanos transcripts occupy unique genomic loci and are expressed with unique temporal profiles during development. Importantly, here we describe and characterize the unique genomic location, conservation, and phylogeny of the Lv ortholog of the well-studied Sp Nanos2. However, in addition to the conserved germline functioning Nanos2, the green sea urchin appears to be an outlier in the echinoderm phyla with eight additional nanos genes. We hypothesize that this expansion of nanos gene members may be the result of a previously uncharacterized L1-class transposon encoded on the opposite strand of a nanos2 pseudogene present on chromosome 12 in this species. The expansion of nanos genes described here represents intriguing insights into germline specification and nanos evolution in this species of sea urchin.
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Affiliation(s)
- Cosmo Pieplow
- MCB Department, Division of Biomedicine, Brown University, Providence RI 02912
| | - Gary Wessel
- MCB Department, Division of Biomedicine, Brown University, Providence RI 02912
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3
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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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Morita S, Ota R, Hayashi M, Kobayashi S. Repression of G1/S Transition by Transient Inhibition of miR-10404 Expression in Drosophila Primordial Germ Cells. iScience 2020; 23:100950. [PMID: 32179474 PMCID: PMC7075979 DOI: 10.1016/j.isci.2020.100950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/20/2020] [Accepted: 02/24/2020] [Indexed: 01/30/2023] Open
Abstract
Cell-cycle quiescence is a common feature of early germline development in many animal species. In Drosophila germline progenitors (pole cells), both G2/M and G1/S transitions are blocked. G2/M transition is repressed by maternal Nanos through suppression of Cyclin B production. However, the molecular mechanism underlying blockage of G1/S transition remains elusive. We found that repression of miR-10404 expression is required to block G1/S transition in pole cells. Expression of miR-10404, a microRNA encoded within the internal transcribed spacer 1 of rDNA, is repressed in early pole cells by maternal polar granule component. This repression delays the degradation of maternal dacapo mRNA, which encodes an inhibitor of G1/S transition. Moreover, derepression of G1/S transition in pole cells causes defects in their maintenance and their migration into the gonads. Our observations reveal the mechanism inhibiting G1/S transition in pole cells and its requirement for proper germline development.
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Affiliation(s)
- Shumpei Morita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Ryoma Ota
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Makoto Hayashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Satoru Kobayashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan.
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5
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Asaoka M, Hanyu-Nakamura K, Nakamura A, Kobayashi S. Maternal Nanos inhibits Importin-α2/Pendulin-dependent nuclear import to prevent somatic gene expression in the Drosophila germline. PLoS Genet 2019; 15:e1008090. [PMID: 31091233 PMCID: PMC6519790 DOI: 10.1371/journal.pgen.1008090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/13/2019] [Indexed: 01/15/2023] Open
Abstract
Repression of somatic gene expression in germline progenitors is one of the critical mechanisms involved in establishing the germ/soma dichotomy. In Drosophila, the maternal Nanos (Nos) and Polar granule component (Pgc) proteins are required for repression of somatic gene expression in the primordial germ cells, or pole cells. Pgc suppresses RNA polymerase II-dependent global transcription in pole cells, but it remains unclear how Nos represses somatic gene expression. Here, we show that Nos represses somatic gene expression by inhibiting translation of maternal importin-α2 (impα2) mRNA. Mis-expression of Impα2 caused aberrant nuclear import of a transcriptional activator, Ftz-F1, which in turn activated a somatic gene, fushi tarazu (ftz), in pole cells when Pgc-dependent transcriptional repression was impaired. Because ftz expression was not fully activated in pole cells in the absence of either Nos or Pgc, we propose that Nos-dependent repression of nuclear import of transcriptional activator(s) and Pgc-dependent suppression of global transcription act as a 'double-lock' mechanism to inhibit somatic gene expression in germline progenitors.
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Affiliation(s)
- Miho Asaoka
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kazuko Hanyu-Nakamura
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Akira Nakamura
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Satoru Kobayashi
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Hanyu-Nakamura K, Matsuda K, Cohen SM, Nakamura A. Pgc suppresses the zygotically acting RNA decay pathway to protect germ plasm RNAs in the Drosophila embryo. Development 2019; 146:dev.167056. [PMID: 30890569 DOI: 10.1242/dev.167056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 03/11/2019] [Indexed: 11/20/2022]
Abstract
Specification of germ cells is pivotal to ensure continuation of animal species. In many animal embryos, germ cell specification depends on maternally supplied determinants in the germ plasm. Drosophila polar granule component (pgc) mRNA is a component of the germ plasm. pgc encodes a small protein that is transiently expressed in newly formed pole cells, the germline progenitors, where it globally represses mRNA transcription. pgc is also required for pole cell survival, but the mechanism linking transcriptional repression to pole cell survival remains elusive. We report that pole cells lacking pgc show premature loss of germ plasm mRNAs, including the germ cell survival factor nanos, and undergo apoptosis. We found that pgc- pole cells misexpress multiple miRNA genes. Reduction of miRNA pathway activity in pgc- embryos partially suppressed germ plasm mRNA degradation and pole cell death, suggesting that Pgc represses zygotic miRNA transcription in pole cells to protect germ plasm mRNAs. Interestingly, germ plasm mRNAs are protected from miRNA-mediated degradation in vertebrates, albeit by a different mechanism. Thus, independently evolved mechanisms are used to silence miRNAs during germ cell specification.
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Affiliation(s)
- Kazuko Hanyu-Nakamura
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan.,Laboratory for Germline Development, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan
| | - Kazuki Matsuda
- Laboratory for Germline Development, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan
| | - Stephen M Cohen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Akira Nakamura
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan .,Laboratory for Germline Development, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan.,Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
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7
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Fefelova EA, Stolyarenko AD, Yakushev EY, Gvozdev VA, Klenov MS. Participation of the piRNA pathway in recruiting a component of RNA polymerase I transcription initiation complex to germline cell nucleoli. Mol Biol 2017. [DOI: 10.1134/s0026893317050089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Robert VJ, Garvis S, Palladino F. Repression of somatic cell fate in the germline. Cell Mol Life Sci 2015; 72:3599-620. [PMID: 26043973 PMCID: PMC11113910 DOI: 10.1007/s00018-015-1942-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 01/13/2023]
Abstract
Germ cells must transmit genetic information across generations, and produce gametes while also maintaining the potential to form all cell types after fertilization. Preventing the activation of somatic programs is, therefore, crucial to the maintenance of germ cell identity. Studies in Caenorhabditis elegans, Drosophila melanogaster, and mouse have revealed both similarities and differences in how somatic gene expression is repressed in germ cells, thereby preventing their conversion into somatic tissues. This review will focus on recent developments in our understanding of how global or gene-specific transcriptional repression, chromatin regulation, and translational repression operate in the germline to maintain germ cell identity and repress somatic differentiation programs.
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Affiliation(s)
- Valérie J Robert
- Ecole Normale Supérieure de Lyon, Université de Lyon, 46 allée d'Italie, 69007, Lyon, France
| | - Steve Garvis
- Ecole Normale Supérieure de Lyon, Université de Lyon, 46 allée d'Italie, 69007, Lyon, France
| | - Francesca Palladino
- Ecole Normale Supérieure de Lyon, Université de Lyon, 46 allée d'Italie, 69007, Lyon, France.
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