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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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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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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: 0.8] [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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4
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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: 0.7] [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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5
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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: 1.6] [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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6
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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: 1.0] [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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7
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Ahuja A, Extavour CG. Patterns of molecular evolution of the germ line specification gene oskar suggest that a novel domain may contribute to functional divergence in Drosophila. Dev Genes Evol 2014; 224:65-77. [PMID: 24407548 DOI: 10.1007/s00427-013-0463-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/07/2013] [Indexed: 01/04/2023]
Abstract
In several metazoans including flies of the genus Drosophila, germ line specification occurs through the inheritance of maternally deposited cytoplasmic determinants, collectively called germ plasm. The novel insect gene oskar is at the top of the Drosophila germ line specification pathway, and also plays an important role in posterior patterning. A novel N-terminal domain of oskar (the Long Oskar domain) evolved in Drosophilids, but the role of this domain in oskar functional evolution is unknown. Trans-species transgenesis experiments have shown that oskar orthologs from different Drosophila species have functionally diverged, but the underlying selective pressures and molecular changes have not been investigated. As a first step toward understanding how Oskar function could have evolved, we applied molecular evolution analysis to oskar sequences from the completely sequenced genomes of 16 Drosophila species from the Sophophora subgenus, Drosophila virilis and Drosophila immigrans. We show that overall, this gene is subject to purifying selection, but that individual predicted structural and functional domains are subject to heterogeneous selection pressures. Specifically, two domains, the Drosophila-specific Long Osk domain and the region that interacts with the germ plasm protein Lasp, are evolving at a faster rate than other regions of oskar. Further, we provide evidence that positive selection may have acted on specific sites within these two domains on the D. virilis branch. Our domain-based analysis suggests that changes in the Long Osk and Lasp-binding domains are strong candidates for the molecular basis of functional divergence between the Oskar proteins of D. melanogaster and D. virilis. This molecular evolutionary analysis thus represents an important step towards understanding the role of an evolutionarily and developmentally critical gene in germ plasm evolution and assembly.
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Affiliation(s)
- Abha Ahuja
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA,
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8
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Ewen-Campen B, Srouji J, Schwager E, Extavour C. oskar Predates the Evolution of Germ Plasm in Insects. Curr Biol 2012; 22:2278-83. [DOI: 10.1016/j.cub.2012.10.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 09/16/2012] [Accepted: 10/09/2012] [Indexed: 01/20/2023]
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9
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Abstract
Translational regulation plays an essential role in many phases of the Drosophila life cycle. During embryogenesis, specification of the developing body pattern requires co-ordination of the translation of oskar, gurken and nanos mRNAs with their subcellular localization. In addition, dosage compensation is controlled by Sex-lethal-mediated translational regulation while dFMR1 (the Drosophila homologue of the fragile X mental retardation protein) controls translation of various mRNAs which function in the nervous system. Here we describe some of the mechanisms that are utilized to regulate these various processes. Our review highlights the complexity that can be involved with multiple factors employing different mechanisms to control the translation of a single mRNA.
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Affiliation(s)
- James E Wilhelm
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21210, USA
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10
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Jambor H, Brunel C, Ephrussi A. Dimerization of oskar 3' UTRs promotes hitchhiking for RNA localization in the Drosophila oocyte. RNA (NEW YORK, N.Y.) 2011; 17:2049-2057. [PMID: 22028360 PMCID: PMC3222118 DOI: 10.1261/rna.2686411] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 08/23/2011] [Indexed: 05/29/2023]
Abstract
mRNA localization coupled with translational control is a highly conserved and widespread mechanism for restricting protein expression to specific sites within eukaryotic cells. In Drosophila, patterning of the embryo requires oskar mRNA transport to the posterior pole of the oocyte and translational repression prior to localization. oskar RNA splicing and the 3' untranslated region (UTR) are required for posterior enrichment of the mRNA. However, reporter RNAs harboring the oskar 3' UTR can localize by hitchhiking with endogenous oskar transcripts. Here we show that the oskar 3' UTR contains a stem-loop structure that promotes RNA dimerization in vitro and hitchhiking in vivo. Mutations in the loop that abolish in vitro dimerization interfere with reporter RNA localization, and restoring loop complementarity restores hitchhiking. Our analysis provides insight into the molecular basis of RNA hitchhiking, whereby localization-incompetent RNA molecules can become locally enriched in the cytoplasm, by virtue of their association with transport-competent RNAs.
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Affiliation(s)
- Helena Jambor
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Christine Brunel
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg Cedex, France
| | - Anne Ephrussi
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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11
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Affiliation(s)
- Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
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12
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Juhn J, Marinotti O, Calvo E, James AA. Gene structure and expression of nanos (nos) and oskar (osk) orthologues of the vector mosquito, Culex quinquefasciatus. INSECT MOLECULAR BIOLOGY 2008; 17:545-52. [PMID: 18828840 PMCID: PMC3721150 DOI: 10.1111/j.1365-2583.2008.00823.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The products of the maternal-effect genes, nanos (nos) and oskar (osk), are important for the development of germ cells in insects. Furthermore, these genes have been proposed as candidates for donating functional DNA regulatory sequences for use in gene drive systems to control transmission of mosquito-borne pathogens. The nos and osk genes of the cosmopolitan vector mosquito, Culex quinquefasciatus, encode proteins with domains common to orthologues found in other mosquitoes. Expression analyses support the conclusion that the role of these genes is conserved generally among members of the nematocera. Hybridization in situ analyses reveal differences in mRNA distribution in early embryos in comparison with the cyclorraphan, Drosophila melanogaster, highlighting a possible feature in the divergence of the clades each insect represents.
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Affiliation(s)
- J Juhn
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
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13
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Roth S. The origin of dorsoventral polarity in Drosophila. Philos Trans R Soc Lond B Biol Sci 2003; 358:1317-29; discussion 1329. [PMID: 14511478 PMCID: PMC1693232 DOI: 10.1098/rstb.2003.1325] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Drosophila dorsoventral (DV) polarity arises during oogenesis when the oocyte nucleus moves from a central posterior to an asymmetrical anterior position. Nuclear movement is a symmetry-breaking step and establishes orthogonality between the anteroposterior and the DV axes. The asymmetrically anchored nucleus defines a cortical region within the oocyte which accumulates high levels of gurken messenger RNA (mRNA) and protein. Gurken is an ovarian-specific member of the transforming growth factor-alpha (TGF-alpha) family of secreted ligands. Secreted Gurken forms a concentration gradient that results in a dorsal-to-ventral gradient of EGF receptor activation in the follicle cells surrounding the oocyte. This leads to concentration-dependent activation or repression of target genes of the EGF pathway in the follicular epithelium. One outcome of this process is the restriction of pipe expression to a ventral domain that comprises 40% of the egg circumference. Pipe presumably modifies extracellular matrix components that are secreted by the follicle cells and are present at the ventral side of embryo after egg deposition. Here, they activate a proteolytic cascade that generates a gradient of the diffusible ligand, Spätzle. Spätzle activates the Toll receptor at the surface of the embryo that stimulates the nuclear uptake of the transcription factor Dorsal. This leads to a nuclear concentration gradient of Dorsal that specifies the cell types along the DV axis of the embryo.
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Affiliation(s)
- Siegfried Roth
- Institut für Entwicklungsbiologie, Universität Köln, Gyrhofstrasse 17, 50923 Köln, Germany.
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14
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Abstract
Transcript localization and translational regulation are two post-transcriptional mechanisms for the spatial and temporal regulation of protein production. During the past year, two transcript localization mechanisms have been elaborated in some detail. Where localization involves directional transport on cytoskeletal tracks, links between the transcripts and the cytoskeletal molecular motors have been elaborated. In the case of localization by generalized transcript degradation combined with localized protection, trans-acting pathways and cis-acting elements for degradation and protection have been identified. A third transcript localization mechanism, vectorial transport out of the nucleus into a particular cytoplasmic domain, was initially thought to localize pair-rule transcripts in Drosophila. However, these have now been shown to be localized by directional transport in the cytoplasm. Transcript localization and translational regulation can be intimately linked in that, for certain messenger RNAs, only the localized fraction of transcripts is translated whereas unlocalized transcripts are translationally repressed. Cis-acting sequences and trans-acting factors that function in translational repression have been identified along with factors involved in relief of translational repression at the site of localization.
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Affiliation(s)
- H D Lipshitz
- Program in Developmental Biology, Research Institute, The Hospital for Sick Children, 555 University Avenue, Ontario M5G 1X8, Toronto, Canada.
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15
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Chang JS, Tan L, Schedl P. The Drosophila CPEB homolog, orb, is required for oskar protein expression in oocytes. Dev Biol 1999; 215:91-106. [PMID: 10525352 DOI: 10.1006/dbio.1999.9444] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The establishment of polarity axes in the Drosophila egg and embryo depends upon the localization and on-site expression of maternal mRNAs. The critical step in the targeting of posterior determinants is the localization of oskar (osk) mRNA to the pole and its on-site translation. Osk protein then recruits other posterior group gene products involved in the formation of pole plasm and in the localization and regulation of the posterior determinant, nanos. Here we have investigated the role of the Drosophila CPEB homolog, the orb gene, in the osk mRNA localization pathway. We demonstrate that the expression of Osk protein is dependent upon the orb gene. In strong orb mutants, Osk protein expression is undetectable, while in the hypomorphic mutant, orb(mel), little or no on-site expression of Osk protein at the posterior pole is observed. The defects in Osk protein accumulation in orb mutant ovaries are correlated with a reduction in the length of the osk poly(A) tails. We show that osk mRNA is in immunoprecipitable complexes with Orb protein in ovaries and that the osk 3' UTR can be UV cross-linked to Orb protein in ovarian extracts. These data suggest that Orb is required to activate the translation of osk mRNA and at that this may be accomplished by a mechanism similar to that used by the Xenopus CPEB protein to control translation of "masked" mRNAs.
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Affiliation(s)
- J S Chang
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, New Jersey, 08544, USA
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16
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Affiliation(s)
- E A Arn
- Department of Biological Sciences, Stanford University, California 94305-5020, USA
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17
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Abstract
Cytoplasmic RNA localization is an evolutionarily ancient mechanism for producing cellular asymmetries. This review considers RNA localization in the context of animal development. Both mRNAs and non-protein-coding RNAs are localized in Drosophila, Xenopus, ascidian, zebrafish, and echinoderm oocytes and embryos, as well as in a variety of developing and differentiated polarized cells from yeast to mammals. Mechanisms used to transport and anchor RNAs in the cytoplasm include vectorial transport out of the nucleus, directed cytoplasmic transport in association with the cytoskeleton, and local entrapment at particular cytoplasmic sites. The majority of localized RNAs are targeted to particular cytoplasmic regions by cis-acting RNA elements; in mRNAs these are almost always in the 3'-untranslated region (UTR). A variety of trans-acting factors--many of them RNA-binding proteins--function in localization. Developmental functions of RNA localization have been defined in Xenopus, Drosophila, and Saccharomyces cerevisiae. In Drosophila, localized RNAs program the antero-posterior and dorso-ventral axes of the oocyte and embryo. In Xenopus, localized RNAs may function in mesoderm induction as well as in dorso-ventral axis specification. Localized RNAs also program asymmetric cell fates during Drosophila neurogenesis and yeast budding.
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Affiliation(s)
- A Bashirullah
- Program in Developmental Biology, Research Institute, Hospital for Sick Children, Toronto, Canada
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18
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Macdonald PM, Kerr K. Mutational analysis of an RNA recognition element that mediates localization of bicoid mRNA. Mol Cell Biol 1998; 18:3788-95. [PMID: 9632762 PMCID: PMC108962 DOI: 10.1128/mcb.18.7.3788] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/1998] [Accepted: 04/03/1998] [Indexed: 02/07/2023] Open
Abstract
Localization signals are RNA regulatory elements that direct the localization of mRNAs to subcellular sites. Localization signals presumably function by mediating RNA recognition events through which the mRNA becomes associated with the localization machinery. At present little is known about individual RNA recognition events, which in turn has limited progress in identifying the trans-acting binding factors involved in these events. Here we describe a detailed characterization of the RNA elements required for the RNA recognition event, event A, that initiates localization of bicoid mRNA in the Drosophila ovary. One element is a helix in which nucleotide identities are not important, suggesting that it plays a primarily structural role. Immediately adjacent to the helix is a recognition domain in which the identities of some, but not all, nucleotides are important for function. Comparison of two related but different RNAs that both support recognition event A further defines the important features of the recognition domain.
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Affiliation(s)
- P M Macdonald
- Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA.
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Webster PJ, Liang L, Berg CA, Lasko P, Macdonald PM. Translational repressor bruno plays multiple roles in development and is widely conserved. Genes Dev 1997; 11:2510-21. [PMID: 9334316 PMCID: PMC316560 DOI: 10.1101/gad.11.19.2510] [Citation(s) in RCA: 178] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/1997] [Accepted: 08/12/1997] [Indexed: 02/05/2023]
Abstract
oskar (osk) mRNA is tightly localized to the posterior pole of the Drosophila oocyte, where the subsequent expression of Osk protein directs abdomen and germ-line formation in the developing embryo. Misplaced expression of Osk protein leads to lethal body patterning defects. The Osk message is translationally repressed before and during the localization process, ensuring that Osk protein is only expressed after the mRNA has reached the posterior. An ovarian protein, Bruno (Bru), has been implicated as a translational repressor of osk mRNA. Here we report the isolation of a cDNA encoding Bru using a novel approach to the expression cloning of an RNA-binding protein, and the identification of previously described mutants in the arrest (aret)-locus as mutants in Bru. The mutant phenotype, along with the binding properties of the protein and its pattern of accumulation within the oocyte, indicate that Bru regulates multiple mRNAs involved in female and male gametogenesis as well as early in embryogenesis. Genetic experiments provide further evidence that Bru functions in the translational repression of osk. Intriguingly, we find that Bru interacts physically with Vasa (Vas), an RNA helicase that is a positive regulator of osk translation. Bru belongs to an evolutionarily conserved family of genes, suggesting that Bru-mediated translational regulation may be widespread. Models for the molecular mechanism of Bru function are discussed.
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Affiliation(s)
- P J Webster
- Department of Biological Sciences, Stanford University, California 94305-5020, USA
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20
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Veyrune JL, Hesketh J, Blanchard JM. 3' untranslated regions of c-myc and c-fos mRNAs: multifunctional elements regulating mRNA translation, degradation and subcellular localization. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 1997; 18:35-63. [PMID: 8994260 DOI: 10.1007/978-3-642-60471-3_3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- J L Veyrune
- Institut de Génétique Moléculaire de Montpellier, CNRS, UMR 5535, Montpellier, France
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21
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Smibert CA, Wilson JE, Kerr K, Macdonald PM. smaug protein represses translation of unlocalized nanos mRNA in the Drosophila embryo. Genes Dev 1996; 10:2600-9. [PMID: 8895661 DOI: 10.1101/gad.10.20.2600] [Citation(s) in RCA: 188] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
nanos mRNA, which encodes the localized component of the Drosophila posterior body patterning determinant, is normally translated only at the posterior pole of the embryo, where the mRNA is concentrated. Here we identify two similar cis-acting sequences in the nanos mRNA 3' untranslated region that mediate translational repression. These sequences bind an embryonic protein of 135 kD, smaug, and we refer to them as smaug recognition elements (SREs). Analysis of point mutations in the SREs reveals a strong correlation between smaug binding and translational repression; mutants unable to bind smaug in vitro are not repressed translationally in vivo, whereas mutants that do bind smaug remain repressed translationally. These results strongly suggest that smaug acts in translational repression of unlocalized nanos mRNA. Translational repression is essential, as embryos expressing a nanos mRNA with mutated SREs develop with anterior body patterning defects and die, despite correct localization of the RNA.
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Affiliation(s)
- C A Smibert
- Department of Biological Sciences, Stanford University, California 94305-5020, USA
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22
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Breitwieser W, Markussen FH, Horstmann H, Ephrussi A. Oskar protein interaction with Vasa represents an essential step in polar granule assembly. Genes Dev 1996; 10:2179-88. [PMID: 8804312 DOI: 10.1101/gad.10.17.2179] [Citation(s) in RCA: 170] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The posterior pole plasm of the Drosophila egg contains the determinants of abdominal and germ-cell fates of the embryo. Pole plasm assembly is induced by oskar RNA localized to the posterior pole of the oocyte. Genetics has revealed three additional genes, staufen, vasa, and tudor, that are also essential for pole plasm formation. Staufen protein is required for both oskar RNA localization and translation. Vasa and Tudor are localized dependent on Oskar protein and are required to accumulate Oskar protein stably at the posterior pole. We have explored interactions between these gene products at the molecular level and find that Oskar interacts directly with Vasa and Staufen, in a yeast two-hybrid assay. These interactions also occur in vitro and are affected by mutations in Oskar that abolish pole plasm formation in vivo. Finally, we show that in the pole plasm, Oskar protein, like Vasa and Tudor, is a component of polar granules, the germ-line-specific RNP structures. These results suggest that the Oskar-Vasa interaction constitutes an initial step in polar granule assembly. In addition, we discuss the possible biological role of the Oskar-Staufen interaction.
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Affiliation(s)
- W Breitwieser
- Developmental Biology Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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23
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Palopoli MF, Patel NH. Neo-Darwinian developmental evolution: can we bridge the gap between pattern and process? Curr Opin Genet Dev 1996; 6:502-8. [PMID: 8791527 DOI: 10.1016/s0959-437x(96)80074-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In the past decade, there has been a surge of renewed interest in the study of developmental evolution. One approach that has been taken is to examine the expression patterns of a candidate gene in divergent taxa and to use these results to infer which aspects of a particular genetic pathway are either conserved or altered. Here we consider this approach from the perspective of the neo-Darwinian paradigm for evolutionary change. If adaptations are typically composed of large numbers of gene substitutions that are of small effect individually, then the candidate gene approach is unlikely to bridge the gap between developmental pattern and evolutionary process: changes in gene expression patterns may identify the steps in developmental pathways that have been altered during evolution but fail to identify the actual genetic changes that have occurred. On the other hand, there is growing support for the view that adaptations often involve large-effect genes; fortunately, the candidate gene approach is well suited to this type of genetic architecture.
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Affiliation(s)
- M F Palopoli
- Howard Hughes Medical Institute, MC1028, AMB N-101, 5841 South Maryland Avenue, Chicago, Illinois 60637, USA.
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24
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Wilson JE, Connell JE, Macdonald PM. aubergine enhances oskar translation in the Drosophila ovary. Development 1996; 122:1631-9. [PMID: 8625849 DOI: 10.1242/dev.122.5.1631] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Although translational regulation of maternal mRNA is important for proper development of the Drosophila embryo, few genes involved in this process have been identified. In this report, we describe the role of aubergine in oskar translation. Previously, aubergine has been implicated in dorsoventral patterning, as eggs from aubergine mutant mothers are ventralized and seldom fertilized (Schupbach, T. and Wieschaus, E. (1991) Genetics 129, 1119–1136). We have isolated two new alleles of aubergine in a novel genetic screen and have shown that aubergine is also required for posterior body patterning, as the small fraction of eggs from aubergine- mothers that are fertilized develop into embryos which lack abdominal segmentation. Although aubergine mutations do not appear to affect the stability of either oskar mRNA or protein, the level of oskar protein is significantly reduced in aubergine mutants. Thus, aubergine is required to enhance oskar translation. While aubergine-dependence is conferred upon oskar mRNA by sequences in the oskar 3′ UTR, aubergine may influence oskar translation through an interaction with sequences upstream of the oskar 3′ UTR.
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Affiliation(s)
- J E Wilson
- Department of Biological Sciences, Stanford University, CA 94305-5020, USA
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Rongo C, Gavis ER, Lehmann R. Localization of oskar RNA regulates oskar translation and requires Oskar protein. Development 1995; 121:2737-46. [PMID: 7555702 DOI: 10.1242/dev.121.9.2737] [Citation(s) in RCA: 146] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The site of oskar RNA and protein localization within the oocyte determines where in the embryo primordial germ cells form and where the abdomen develops. Initiation of oskar RNA localization requires the activity of several genes. We show that ovaries mutant for any of these genes lack Oskar protein. Using various transgenic constructs we have determined that sequences required for oskar RNA localization and translational repression map to the oskar 3′UTR, while sequences involved in the correct temporal activation of translation reside outside the oskar 3′UTR. Upon localization of oskar RNA and protein at the posterior pole, Oskar protein is required to maintain localization of oskar RNA throughout oogenesis. Stable anchoring of a transgenic reporter RNA at the posterior pole is disrupted by oskar nonsense mutations. We propose that initially localization of oskar RNA permits translation into Oskar protein and that subsequently Oskar protein regulates its own RNA localization through a positive feedback mechanism.
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Affiliation(s)
- C Rongo
- Whitehead Institute for Biomedical Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge 02142, USA
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Blanchet-Tournier MF, Tricoire H, Busson D, Lamour-Isnard C. The segment-polarity gene fused is highly conserved in Drosophila. Gene X 1995; 161:157-62. [PMID: 7665071 DOI: 10.1016/0378-1119(95)00219-v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The segment polarity gene fused (fu) is involved in specification of positional information inside embryonic segments in Drosophila melanogaster (Dm). The predicted Fused (Fu) protein contains a serine/threonine kinase domain and a second domain with unknown function. We cloned and sequenced the fu homologous gene from Drosophila virilis (Dv) and made an interspecific DNA sequence comparison to identify regions that have been conserved during evolution. Comparison of the predicted amino acid (aa) sequences reveals two regions of strong homology, one corresponding to the kinase domain (268 aa), the other located in the third exon of the Dm fu gene, suggesting a functional importance for this region. Stretches of significantly conserved sequences are also observed in the 5' and 3' untranslated regions. Weak homology is seen in the intronic sequences although the adjacent exonic sequences are mostly conserved. These findings indicate a high conservation of the predicted Fu protein during the evolution of Drosophila.
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Kim-Ha J, Kerr K, Macdonald PM. Translational regulation of oskar mRNA by bruno, an ovarian RNA-binding protein, is essential. Cell 1995; 81:403-12. [PMID: 7736592 DOI: 10.1016/0092-8674(95)90393-3] [Citation(s) in RCA: 358] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Oskar (osk) protein directs the deployment of nanos (nos), the posterior body-patterning morphogen in Drosophila. To avoid inappropriate activation of nos, osk activity must appear only at the posterior pole of the oocyte, where the osk mRNA becomes localized during oogenesis. Here, we show that translation of osk mRNA is, and must be, repressed prior to its localization; absence of repression allows osk protein to accumulate throughout the oocyte, specifying posterior body patterning throughout the embryo. Translational repression is mediated by an ovarian protein, bruno, that binds specifically to bruno response elements (BREs), present in multiple copies in the osk mRNA 3'UTR. Addition of BREs to a heterologous mRNA renders it sensitive to translational repression in the ovary.
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Affiliation(s)
- J Kim-Ha
- Department of Biological Sciences, Stanford University, California 94305-5020, USA
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Abstract
Rapid advances have been made in the understanding of the genetic basis of development and pattern formation in a variety of model systems. By examining the extent to which these developmental systems are conserved or altered between different organisms, insight can be gained into the evolutionary events that have generated the diversity of organisms around us. The molecular and genetic basis of early pattern formation in Drosophila melanogaster has been particularly well studied, and comparisons to other insects have revealed conservation of some aspects of development, as well as differences that may explain variations in early patterning events.
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Affiliation(s)
- N H Patel
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21210-3399
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