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O’Connell LC, Johnson V, Hutton AK, Otis JP, Murthy AC, Liang MC, Wang SH, Fawzi NL, Mowry KL. Intrinsically disordered regions and RNA binding domains contribute to protein enrichment in biomolecular condensates in Xenopus oocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566489. [PMID: 37986933 PMCID: PMC10659413 DOI: 10.1101/2023.11.10.566489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Proteins containing both intrinsically disordered regions (IDRs) and RNA binding domains (RBDs) can phase separate in vitro, forming bodies similar to cellular biomolecular condensates. However, how IDR and RBD domains contribute to in vivo recruitment of proteins to biomolecular condensates remains poorly understood. Here, we analyzed the roles of IDRs and RBDs in L-bodies, biomolecular condensates present in Xenopus oocytes. We show that a cytoplasmic isoform of hnRNPAB, which contains two RBDs and an IDR, is highly enriched in L-bodies. While both of these domains contribute to hnRNPAB self-association and phase separation in vitro and mediate enrichment into L-bodies in oocytes, neither the RBDs nor the IDR replicate the localization of full-length hnRNPAB. Our results suggest a model where the additive effects of the IDR and RBDs regulate hnRNPAB partitioning into L-bodies. This model likely has widespread applications as proteins containing RBD and IDR domains are common biomolecular condensate residents.
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Affiliation(s)
- Liam C. O’Connell
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University Providence, RI 02912, USA
| | - Victoria Johnson
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University Providence, RI 02912, USA
| | - Anika K. Hutton
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University Providence, RI 02912, USA
| | - Jessica P. Otis
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University Providence, RI 02912, USA
| | - Anastasia C. Murthy
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University Providence, RI 02912, USA
| | - Mark C. Liang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University Providence, RI 02912, USA
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University Providence, RI 02912, USA
| | - Nicolas L. Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University Providence, RI 02912, USA
| | - Kimberly L. Mowry
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University Providence, RI 02912, USA
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2
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Multivalent interactions with RNA drive recruitment and dynamics in biomolecular condensates in Xenopus oocytes. iScience 2022; 25:104811. [PMID: 35982794 PMCID: PMC9379569 DOI: 10.1016/j.isci.2022.104811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/24/2022] [Accepted: 07/16/2022] [Indexed: 11/22/2022] Open
Abstract
RNA localization and biomolecular condensate formation are key biological strategies for organizing the cytoplasm and generating cellular polarity. In Xenopus oocytes, RNAs required for germ layer patterning localize in biomolecular condensates, termed Localization bodies (L-bodies). Here, we have used an L-body RNA-binding protein, PTBP3, to test the role of RNA–protein interactions in regulating the biophysical characteristics of L-bodies in vivo and PTBP3–RNA condensates in vitro. Our results reveal that RNA–protein interactions drive recruitment of PTBP3 and localized RNA to L-bodies and that multivalent interactions tune the dynamics of the PTBP3 after localization. In a concentration-dependent manner, RNA becomes non-dynamic and interactions with the RNA determine PTBP3 dynamics within these biomolecular condensates in vivo and in vitro. Importantly, RNA, and not protein, is required for maintenance of the PTBP3–RNA condensates in vitro, pointing to a model where RNA serves as a non-dynamic substructure in these condensates. RNA–protein interactions drive recruitment of both RNA and protein to L-bodies RNA is non-dynamic in both L-bodies and in vitro condensates Multivalent interactions with RNA tune protein dynamics both in vivo and in vitro RNA, but not protein, is required for maintenance of the in vitro condensates
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3
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Evolutionary conservation of maternal RNA localization in fishes and amphibians revealed by TOMO-Seq. Dev Biol 2022; 489:146-160. [PMID: 35752299 DOI: 10.1016/j.ydbio.2022.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/18/2022] [Accepted: 06/19/2022] [Indexed: 11/24/2022]
Abstract
Asymmetrical localization of biomolecules inside the egg, results in uneven cell division and establishment of many biological processes, cell types and the body plan. However, our knowledge about evolutionary conservation of localized transcripts is still limited to a few models. Our goal was to compare localization profiles along the animal-vegetal axis of mature eggs from four vertebrate models, two amphibians (Xenopus laevis, Ambystoma mexicanum) and two fishes (Acipenser ruthenus, Danio rerio) using the spatial expression method called TOMO-Seq. We revealed that RNAs of many known important transcripts such as germ layer determinants, germ plasm factors and members of key signalling pathways, are localized in completely different profiles among the models. It was also observed that there was a poor correlation between the vegetally localized transcripts but a relatively good correlation between the animally localized transcripts. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model.
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4
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Ponomarev MB, Konduktorova VV, Luchinskaya NN, Belyavsky AV. Localization of Germes RNA in Xenopus Oocytes. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421010057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Abstract
RNA localization is a key biological strategy for organizing the cytoplasm and generating both cellular and developmental polarity. During RNA localization, RNAs are targeted asymmetrically to specific subcellular destinations, resulting in spatially and temporally restricted gene expression through local protein synthesis. First discovered in oocytes and embryos, RNA localization is now recognized as a significant regulatory strategy for diverse RNAs, both coding and non-coding, in a wide range of cell types. Yet, the highly polarized cytoplasm of the oocyte remains a leading model to understand not only the principles and mechanisms underlying RNA localization, but also links to the formation of biomolecular condensates through phase separation. Here, we discuss both RNA localization and biomolecular condensates in oocytes with a particular focus on the oocyte of the frog, Xenopus laevis.
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Affiliation(s)
- Sarah E Cabral
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States
| | - Kimberly L Mowry
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States.
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6
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Sindelka R, Abaffy P, Qu Y, Tomankova S, Sidova M, Naraine R, Kolar M, Peuchen E, Sun L, Dovichi N, Kubista M. Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan. Sci Rep 2018; 8:8315. [PMID: 29844480 PMCID: PMC5974320 DOI: 10.1038/s41598-018-26592-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/08/2018] [Indexed: 12/24/2022] Open
Abstract
Asymmetric cell division is a ubiquitous feature during the development of higher organisms. Asymmetry is achieved by differential localization or activities of biological molecules such as proteins, and coding and non-coding RNAs. Here, we present subcellular transcriptomic and proteomic analyses along the animal-vegetal axis of Xenopus laevis eggs. More than 98% of the maternal mRNAs could be categorized into four localization profile groups: animal, vegetal, extremely vegetal, and a newly described group of mRNAs that we call extremely animal, which are mRNAs enriched in the animal cortex region. 3′UTRs of localized mRNAs were analyzed for localization motifs. Several putative motifs were discovered for vegetal and extremely vegetal mRNAs, while no distinct conserved motifs for the extremely animal mRNAs were identified, suggesting different localization mechanisms. Asymmetric profiles were also found for proteins, with correlation to those of corresponding mRNAs. Based on unexpected observation of the profiles of the homoeologous genes exd2 we propose a possible mechanism of genetic evolution.
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Affiliation(s)
- Radek Sindelka
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic.
| | - Pavel Abaffy
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Yanyan Qu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Silvie Tomankova
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Monika Sidova
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Ravindra Naraine
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Michal Kolar
- Institute of Molecular Genetics, Videnska 1083, 142 20, Prague 4, Czech Republic
| | - Elizabeth Peuchen
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Norman Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Mikael Kubista
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic.,TATAA Biocenter, Odinsgatan 28, Göteborg, 411 03, Sweden
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7
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Sindelka R, Sidova M, Abaffy P, Kubista M. Asymmetric Localization and Distribution of Factors Determining Cell Fate During Early Development of Xenopus laevis. Results Probl Cell Differ 2017; 61:229-241. [PMID: 28409307 DOI: 10.1007/978-3-319-53150-2_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Asymmetric division is a property of eukaryotic cells that is fundamental to the formation of higher life forms. Despite its importance, the mechanism behind it remains elusive. Asymmetry in the cell is induced by polarization of cell fate determinants that become unevenly distributed among progeny cells. So far dozens of determinants have been identified. Xenopus laevis is an ideal system to study asymmetric cell division during early development, because of the huge size of its oocytes and early-stage blastomeres. Here, we present the current knowledge about localization and distribution of cell fate determinants along the three body axes: animal-vegetal, dorsal-ventral, and left-right. Uneven distribution of cell fate determinants during early development specifies the formation of the embryonic body plan.
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Affiliation(s)
- Radek Sindelka
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic-Biocev, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Monika Sidova
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic-Biocev, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Pavel Abaffy
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic-Biocev, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic-Biocev, Prumyslova 595, 252 50, Vestec, Czech Republic.
- TATAA Biocenter AB, Odinsgatan 28, 411 03, Göteborg, Sweden.
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8
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Localization in Oogenesis of Maternal Regulators of Embryonic Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 953:173-207. [DOI: 10.1007/978-3-319-46095-6_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Roussis IM, Guille M, Myers FA, Scarlett GP. RNA Whole-Mount In situ Hybridisation Proximity Ligation Assay (rISH-PLA), an Assay for Detecting RNA-Protein Complexes in Intact Cells. PLoS One 2016; 11:e0147967. [PMID: 26824753 PMCID: PMC4732756 DOI: 10.1371/journal.pone.0147967] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/11/2016] [Indexed: 11/19/2022] Open
Abstract
Techniques for studying RNA-protein interactions have lagged behind those for DNA-protein complexes as a consequence of the complexities associated with working with RNA. Here we present a method for the modification of the existing In Situ Hybridisation-Proximity Ligation Assay (ISH-PLA) protocol to adapt it to the study of RNA regulation (rISH-PLA). As proof of principle we used the well-characterised interaction of the Xenopus laevis Staufen RNA binding protein with Vg1 mRNA, the complex of which co-localises to the vegetal pole of Xenopus oocytes. The applicability of both the Stau1 antibody and the Locked Nucleic Acid probe (LNA) recognising Vg1 mRNA were independently validated by whole-mount Immunohistochemistry and whole-mount in situ hybridisation assays respectively prior to combining them in the rISH-PLA assay. The rISH-PLA assay allows the identification of a given RNA-protein complex at subcellular and single cell resolution, thus avoiding the lack of spatial resolution and sensitivity associated with assaying heterogenous cell populations from which conventional RNA-protein interaction detection techniques suffer. This technique will be particularly usefully for studying the activity of RNA binding proteins (RBPs) in complex mixtures of cells, for example tissue sections or whole embryos.
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Affiliation(s)
- Ioannis M. Roussis
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
| | - Matthew Guille
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
| | - Fiona A. Myers
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
| | - Garry P. Scarlett
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
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10
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Abstract
The germ cell lineage in Xenopus is specified by the inheritance of germ plasm that assembles within the mitochondrial cloud or Balbiani body in stage I oocytes. Specific RNAs, such as nanos1, localize to the germ plasm. nanos1 has the essential germline function of blocking somatic gene expression and thus preventing Primordial Germ Cell (PGC) loss and sterility. Hermes/Rbpms protein and nanos RNA co-localize within germinal granules, diagnostic electron dense particles found within the germ plasm. Previous work indicates that nanos accumulates within the germ plasm through a diffusion/entrapment mechanism. Here we show that Hermes/Rbpms interacts with nanos through sequence specific RNA localization signals found in the nanos-3'UTR. Importantly, Hermes/Rbpms specifically binds nanos, but not Vg1 RNA in the nucleus of stage I oocytes. In vitro binding data show that Hermes/Rbpms requires additional factors that are present in stage I oocytes in order to bind nanos1. One such factor may be hnRNP I, identified in a yeast-2-hybrid screen as directly interacting with Hermes/Rbpms. We suggest that Hermes/Rbpms functions as part of a RNP complex in the nucleus that facilitates selection of germline RNAs for germ plasm localization. We propose that Hermes/Rbpms is required for nanos RNA to form within the germinal granules and in this way, participates in the germline specific translational repression and sequestration of nanos RNA.
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11
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Claußen M, Lingner T, Pommerenke C, Opitz L, Salinas G, Pieler T. Global analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus species. Mol Biol Cell 2015; 26:3777-87. [PMID: 26337391 PMCID: PMC4626063 DOI: 10.1091/mbc.e15-02-0115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 08/28/2015] [Indexed: 12/27/2022] Open
Abstract
Subcellular localization of mRNAs contributes to the generation of cellular asymmetries and cell fate determination. A comparative global analysis is given of animally and vegetally enriched RNAs in oocytes from two closely related Xenopus species. RNAs that localize to the vegetal cortex during Xenopus laevis oogenesis have been reported to function in germ layer patterning, axis determination, and development of the primordial germ cells. Here we report on the genome-wide, comparative analysis of differentially localizing RNAs in Xenopus laevis and Xenopus tropicalis oocytes, revealing a surprisingly weak degree of conservation in respect to the identity of animally as well as vegetally enriched transcripts in these closely related species. Heterologous RNA injections and protein binding studies indicate that the different RNA localization patterns in these two species are due to gain/loss of cis-acting localization signals rather than to differences in the RNA-localizing machinery.
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Affiliation(s)
- Maike Claußen
- Institute of Developmental Biochemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Thomas Lingner
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Claudia Pommerenke
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Lennart Opitz
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Gabriela Salinas
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Tomas Pieler
- Institute of Developmental Biochemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
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12
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Intracellular microRNA profiles form in the Xenopus laevis oocyte that may contribute to asymmetric cell division. Sci Rep 2015; 5:11157. [PMID: 26059897 PMCID: PMC4461913 DOI: 10.1038/srep11157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/18/2015] [Indexed: 12/17/2022] Open
Abstract
Asymmetric distribution of fate determinants within cells is an essential biological strategy to prepare them for asymmetric division. In this work we measure the intracellular distribution of 12 maternal microRNAs (miRNA) along the animal-vegetal axis of the Xenopus laevis oocyte using qPCR tomography. We find the miRNAs have distinct intracellular profiles that resemble two out of the three profiles we previously observed for mRNAs. Our results suggest that miRNAs in addition to proteins and mRNAs may have asymmetric distribution within the oocyte and may contribute to asymmetric cell division as cell fate determinants.
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13
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Re A, Joshi T, Kulberkyte E, Morris Q, Workman CT. RNA-protein interactions: an overview. Methods Mol Biol 2014; 1097:491-521. [PMID: 24639174 DOI: 10.1007/978-1-62703-709-9_23] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
RNA binding proteins (RBPs) are key players in the regulation of gene expression. In this chapter we discuss the main protein-RNA recognition modes used by RBPs in order to regulate multiple steps of RNA processing. We discuss traditional and state-of-the-art technologies that can be used to study RNAs bound by individual RBPs, or vice versa, for both in vitro and in vivo methodologies. To help highlight the biological significance of RBP mediated regulation, online resources on experimentally verified protein-RNA interactions are briefly presented. Finally, we present the major tools to computationally infer RNA binding sites according to the modeling features and to the unsupervised or supervised frameworks that are adopted. Since some RNA binding site search algorithms are derived from DNA binding site search algorithms, we discuss the commonalities and novelties introduced to handle both sequence and structural features uniquely characterizing protein-RNA interactions.
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Affiliation(s)
- Angela Re
- University of Trento, Mattarello, Italy
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14
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Yasuda K, Kotani T, Yamashita M. A cis-acting element in the coding region of cyclin B1 mRNA couples subcellular localization to translational timing. Dev Biol 2013; 382:517-29. [DOI: 10.1016/j.ydbio.2013.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 05/09/2013] [Accepted: 05/13/2013] [Indexed: 12/20/2022]
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15
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Nijjar S, Woodland HR. Localisation of RNAs into the germ plasm of vitellogenic Xenopus oocytes. PLoS One 2013; 8:e61847. [PMID: 23626739 PMCID: PMC3633952 DOI: 10.1371/journal.pone.0061847] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/14/2013] [Indexed: 11/21/2022] Open
Abstract
We have studied the localisation of mRNAs in full-grown Xenopus laevis oocytes by injecting fluorescent RNAs, followed by confocal microscopy of the oocyte cortex. Concentrating on RNA encoding the Xenopus Nanos homologue, nanos1 (formerly Xcat2), we find that it consistently localised into aggregated germ plasm ribonucleoprotein (RNP) particles, independently of cytoskeletal integrity. This implies that a diffusion/entrapment-mediated mechanism is active, as previously reported for previtellogenic oocytes. Sometimes this was accompanied by localisation into scattered particles of the “late”, Vg1/VegT pathway; occasionally only late pathway localisation was seen. The Xpat RNA behaved in an identical fashion and for neither RNA was the localisation changed by any culture conditions tested. The identity of the labelled RNP aggregates as definitive germ plasm was confirmed by their inclusion of abundant mitochondria and co-localisation with the germ plasm protein Hermes. Further, the nanos1/Hermes RNP particles are interspersed with those containing the germ plasm protein Xpat. These aggregates may be followed into the germ plasm of unfertilized eggs, but with a notable reduction in its quantity, both in terms of injected molecules and endogenous structures. Our results conflict with previous reports that there is no RNA localisation in large oocytes, and that during mid-oogenesis even germ plasm RNAs localise exclusively by the late pathway. We find that in mid oogenesis nanos1 RNA also localises to germ plasm but also by the late pathway. Late pathway RNAs, Vg1 and VegT, also may localise into germ plasm. Our results support the view that mechanistically the two modes of localisation are extremely similar, and that in an injection experiment RNAs might utilise either pathway, the distinction in fates being very subtle and subject to variation. We discuss these results in relation to their biological significance and the results of others.
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Affiliation(s)
- Sarbjit Nijjar
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Hugh R. Woodland
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- * E-mail:
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16
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Regulation of cell polarity and RNA localization in vertebrate oocytes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 306:127-85. [PMID: 24016525 DOI: 10.1016/b978-0-12-407694-5.00004-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It has long been appreciated that the inheritance of maternal cytoplasmic determinants from different regions of the egg can lead to differential specification of blastomeres during cleavage. Localized RNAs are important determinants of cell fate in eggs and embryos but are also recognized as fundamental regulators of cell structure and function. This chapter summarizes recent molecular and genetic experiments regarding: (1) mechanisms that regulate polarity during different stages of vertebrate oogenesis, (2) pathways that localize presumptive protein and RNA determinants within the polarized oocyte and egg, and (3) how these determinants act in the embryo to determine the ultimate cell fates. Emphasis is placed on studies done in Xenopus, where extensive work has been done in these areas, and comparisons are drawn with fish and mammals. The prospects for future work using in vivo genome manipulation and other postgenomic approaches are also discussed.
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17
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Farooq M, Choi J, Seoane AI, Lleras RA, Tran HV, Mandal SA, Nelson CL, Soto JG. Identification of 3'UTR sequence elements and a teloplasm localization motif sufficient for the localization of Hro-twist mRNA to the zygotic animal and vegetal poles. Dev Growth Differ 2012; 54:519-34. [PMID: 22587329 DOI: 10.1111/j.1440-169x.2012.01352.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The early localization of mRNA transcripts is critical in sorting cell fate determinants in the developing embryo. In the glossiphoniid leech, Helobdella robusta, maternal mRNAs, such as Hro-twist, localize to the zygotic teloplasm. Ten seven nucleotide repeat elements (AAUAAUA) called ARE2 and a predicted secondary structural motif, called teloplasm localization motif (TLM), are present in the 3'UTR of Hro-twist mRNA. We used site-directed mutagenesis, deletions, and microinjection of labeled, exogenous transcripts to determine if ARE2 elements, and the TLM, play a role in Hro-twist mRNA localization. Deleting the poly-A tail and the cytoplasmic polyadenylation element (CPE) had no effect on Hro-twist mRNA localization. Site-directed mutagenesis of nucleotides that altered ARE2 element sequences or the TLM suggest that the ARE2 elements and the TLM are important for Hro-twist mRNA localization to the teloplasm of pre-cleavage zygotes. Hro-Twist protein expression data suggest that the localization of Hro-twist transcripts in zygotes and stage two embryos is not involved in ensuring mesoderm specification, as Hro-Twist protein is expressed uniformly in most cells before gastrulation. Our data may support a shared molecular mechanism for leech transcripts that localize to the teloplasm.
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Affiliation(s)
- Mehrin Farooq
- Biological Sciences Department, San Jose State University, San Jose, CA 95192-0100, USA
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18
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Gonsalvez GB, Long RM. Spatial regulation of translation through RNA localization. F1000 BIOLOGY REPORTS 2012; 4:16. [PMID: 22912650 PMCID: PMC3412389 DOI: 10.3410/b4-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA localization is a mechanism to post-transcriptionally regulate gene
expression. Eukaryotic organisms ranging from fungi to mammals localize mRNAs to
spatially restrict synthesis of specific proteins to distinct regions of the
cytoplasm. In this review, we provide a general summary of RNA localization
pathways in Saccharomyces cerevisiae, Xenopus,
Drosophila and mammalian neurons.
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Affiliation(s)
- Graydon B. Gonsalvez
- Department of Cellular Biology and
Anatomy, Georgia Health Sciences UniversityC2915D,
1459 Laney Walker Blvd., Augusta, GA
30912USA
| | - Roy M. Long
- Department of Microbiology, Immunology
& Molecular Genetics, Medical College of
Wisconsin8701 Watertown Plank Rd., Milwaukee, WI
53226USA
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19
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Shahbabian K, Chartrand P. Control of cytoplasmic mRNA localization. Cell Mol Life Sci 2012; 69:535-52. [PMID: 21984598 PMCID: PMC11115051 DOI: 10.1007/s00018-011-0814-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 08/09/2011] [Accepted: 09/01/2011] [Indexed: 12/17/2022]
Abstract
mRNA localization is a mechanism used by various organisms to control the spatial and temporal production of proteins. This process is a highly regulated event that requires multiple cis- and trans-acting elements that mediate the accurate localization of target mRNAs. The intrinsic nature of localization elements, together with their interaction with different RNA-binding proteins, establishes control mechanisms that can oversee the transcript from its birth in the nucleus to its specific final destination. In this review, we aim to summarize the different mechanisms of mRNA localization, with a particular focus on the various control mechanisms that affect the localization of mRNAs in the cytoplasm.
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Affiliation(s)
- Karen Shahbabian
- Department of Biochemistry, Université de Montréal, 2900 Edouard-Montpetit, Montréal, Qc Canada
| | - Pascal Chartrand
- Department of Biochemistry, Université de Montréal, 2900 Edouard-Montpetit, Montréal, Qc Canada
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King ML, Messitt TJ, Mowry KL. Putting RNAs in the right place at the right time: RNA localization in the frog oocyte. Biol Cell 2012; 97:19-33. [PMID: 15601255 DOI: 10.1042/bc20040067] [Citation(s) in RCA: 243] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Localization of maternal mRNAs in many developing organisms provides the basis for both initial polarity during oogenesis and patterning during embryogenesis. Prominent examples of this phenomenon are found in Xenopus laevis, where localized maternal mRNAs generate developmental polarity along the animal/vegetal axis. Targeting of mRNA molecules to specific subcellular regions is a fundamental mechanism for spatial regulation of gene expression, and considerable progress has been made in defining the underlying molecular pathways.
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Affiliation(s)
- Mary Lou King
- Department of Cell Biology and Anatomy, University of Miami School of Medicine, 1011 NW 15th St., Miami, FL 33136, USA.
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21
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Safe Keeping the Message: mRNP Complexes Tweaking after Transcription. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 722:118-36. [DOI: 10.1007/978-1-4614-0332-6_8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
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22
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Claussen M, Pieler T. Identification of vegetal RNA-localization elements in Xenopus oocytes. Methods 2010; 51:146-51. [PMID: 20178845 DOI: 10.1016/j.ymeth.2010.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 02/15/2010] [Accepted: 02/16/2010] [Indexed: 11/17/2022] Open
Abstract
Localized mRNAs have been identified in a large variety of cell types where they contribute to the establishment of cell asymmetries and can function as cell fate determinants. In Xenopus, RNAs that localize to the vegetal cortex during oogenesis function in early embryonic patterning as well as in the development of primordial germ cells. Based on their temporal and spatial localization patterns, vegetally localizing RNAs are referred to as either early-pathway RNAs which transiently localize in the mitochondrial cloud, or as late-pathway RNAs. Vegetal RNA-localization is driven by cis-acting signal sequences that, in most cases, were found to reside in the 3'-UTRs and which are recognized by trans-acting localization factors. Here we describe the methods of how vegetal RNA-localization elements can be identified by injection of fluorescently-labeled or tagged RNAs.
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Affiliation(s)
- Maike Claussen
- Department of Developmental Biochemistry, Göttingen Center for Molecular Biosciences, Justus-von-Liebig-Weg 11, Göttingen, Germany
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23
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Hannapel DJ. A model system of development regulated by the long-distance transport of mRNA. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2010; 52:40-52. [PMID: 20074139 DOI: 10.1111/j.1744-7909.2010.00911.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
BEL1-like transcription factors are ubiquitous in plants and interact with KNOTTED1-types to regulate numerous developmental processes. In potato, the RNA of several BEL1-like transcription factors has been identified in phloem cells. One of these, StBEL5, and its Knox protein partner regulate tuber formation by targeting genes that control growth. RNA detection methods and grafting experiments demonstrated that StBEL5 transcripts move across a graft union to localize in stolon tips, the site of tuber induction. This movement of RNA originates in source leaf veins and petioles and is induced by a short-day photoperiod, regulated by the untranslated regions, and correlated with enhanced tuber production. Addition of the StBEL5 untranslated regions to another BEL1-like mRNA resulted in its preferential transport to stolon tips leading to increased tuber production. Upon fusion of the untranslated regions of StBEL5 to a beta-glucuronidase marker, translation in tobacco protoplasts was repressed by those constructs containing the 3' untranslated sequence. The untranslated regions of the StBEL5 mRNA are involved in mediating its long-distance transport and in controlling translation. The 3' untranslated sequence contains an abundance of conserved motifs that may serve as binding motifs for RNA-binding proteins. Because of their presence in the phloem sieve tube system, their unique untranslated region sequences and their diverse RNA accumulation patterns, the family of BEL1-like RNAs from potato represents a valuable model for studying the long-distance transport of full-length mRNAs and their role in development.
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Affiliation(s)
- David J Hannapel
- Plant Biology Major, 253 Horticulture Hall, Iowa State University, Ames, IA 50011-1100, USA.
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24
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Skern-Mauritzen R, Frost P, Dalvin S, Kvamme BO, Sommerset I, Nilsen F. A trypsin-like protease with apparent dual function in early Lepeophtheirus salmonis (Krøyer) development. BMC Mol Biol 2009; 10:44. [PMID: 19439101 PMCID: PMC2689223 DOI: 10.1186/1471-2199-10-44] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 05/13/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypsin-like serine proteases are involved in a large number of processes including digestive degradation, regulation of developmental processes, yolk degradation and yolk degradome activation. Trypsin like peptidases considered to be involved in digestion have been characterized in Lepeophtheirus salmonis. During these studies a trypsin-like peptidase which differed in a number of traits were identified. RESULTS An intronless trypsin-like serine peptidase (LsTryp10) from L., salmonis was identified and characterized. LsTryp10 mRNA is evenly distributed in the ovaries and oocytes, but is located along the ova periphery. LsTryp10 protein is deposited in the oocytes and all embryonic cells. LsTryp10 mRNA translation and concurrent degradation after fertilization was found in the embryos demonstrating that LsTryp10 protein is produced both by the embryo and maternally. The results furthermore indicate that LsTryp10 protein of maternal origin has a distribution pattern different to that of embryonic origin. CONCLUSION Based on present data and previous studies of peptidases in oocytes and embryos, we hypothesize that maternally deposited LsTryp10 protein is involved in regulation of the yolk degradome. The function of LsTryp10 produced by the embryonic cells remains unknown. To our knowledge a similar expression pattern has not previously been reported for any protease.
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Affiliation(s)
- Rasmus Skern-Mauritzen
- Department of Population Genetics and Ecology, Institute of Marine Research, 5817 Bergen, Norway
| | - Petter Frost
- Department of Population Genetics and Ecology, Institute of Marine Research, 5817 Bergen, Norway
- Intervet Norbio AS, 5008 Bergen, Norway
| | - Sussie Dalvin
- Department of Population Genetics and Ecology, Institute of Marine Research, 5817 Bergen, Norway
| | - Bjørn Olav Kvamme
- Department of Health, Institute of Marine Research, 5817 Bergen, Norway
| | | | - Frank Nilsen
- Department of Population Genetics and Ecology, Institute of Marine Research, 5817 Bergen, Norway
- Department of Biology, University of Bergen, 5020 Bergen, Norway
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25
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Abstract
The localization of mRNAs to subcellular compartments provides a mechanism for regulating gene expression with exquisite temporal and spatial control. Recent studies suggest that a large fraction of mRNAs localize to distinct cytoplasmic domains. In this Review, we focus on cis-acting RNA localization elements, RNA-binding proteins, and the assembly of mRNAs into granules that are transported by molecular motors along cytoskeletal elements to their final destination in the cell.
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Affiliation(s)
- Kelsey C Martin
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095-1737, USA.
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26
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Farley BM, Ryder SP. Regulation of Maternal mRNAs in Early Development. Crit Rev Biochem Mol Biol 2008; 43:135-62. [PMID: 18365862 DOI: 10.1080/10409230801921338] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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27
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PTB/hnRNP I is required for RNP remodeling during RNA localization in Xenopus oocytes. Mol Cell Biol 2007; 28:678-86. [PMID: 18039852 DOI: 10.1128/mcb.00999-07] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transport of specific mRNAs to defined regions within the cell cytoplasm is a fundamental mechanism for regulating cell and developmental polarity. In the Xenopus oocyte, Vg1 RNA is transported to the vegetal cytoplasm, where localized expression of the encoded protein is critical for embryonic polarity. The Vg1 localization pathway is directed by interactions between key motifs within Vg1 RNA and protein factors recognizing those RNA sequences. We have investigated how RNA-protein interactions could be modulated to trigger distinct steps in the localization pathway and found that the Vg1 RNP is remodeled during cytoplasmic RNA transport. Our results implicate two RNA-binding proteins with key roles in Vg1 RNA localization, PTB/hnRNP I and Vg1RBP/vera, in this process. We show that PTB/hnRNP I is required for remodeling of the interaction between Vg1 RNA and Vg1RBP/vera. Critically, mutations that block this remodeling event also eliminate vegetal localization of the RNA, suggesting that RNP remodeling is required for localization.
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28
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Oberman F, Rand K, Maizels Y, Rubinstein AM, Yisraeli JK. VICKZ proteins mediate cell migration via their RNA binding activity. RNA (NEW YORK, N.Y.) 2007; 13:1558-69. [PMID: 17652133 PMCID: PMC1950752 DOI: 10.1261/rna.559507] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The highly conserved, RNA binding VICKZ proteins help regulate RNA localization, stability, and translation in many eukaryotes. These proteins are also required for cell migration in embryos and cultured cells. In adults, many tumors overexpress VICKZ homologs, and it has been hypothesized that the proteins can mediate cell motility and invasion. How these proteins facilitate cell movement and, in particular, whether their ability to bind RNA plays a role in their function remain unclear. Using HPLC and mass spectrometry to identify a region of Xenopus Vg1 RBP (xVICKZ3) that binds the vegetal localization element of Vg1 RNA, we generated a deletion construct that functions in a dominant-negative manner. The construct associates with full-length xVICKZ3 and severely reduces binding to target RNAs. This dominant-negative construct phenocopies the effect of down-regulating xVICKZ3 in Xenopus embryos. A corresponding deletion in the human homolog hVICKZ1 similarly functions in a dominant-negative fashion to reduce the ability of full-length hVICKZ protein to bind RNA. Expression of the dominant-negative construct in human carcinoma cells inhibits cell movement by several criteria. We conclude that the ability of VICKZ proteins to mediate cell migration, in vitro and in vivo, requires their RNA binding activity.
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Affiliation(s)
- Froma Oberman
- Department of Anatomy and Cell Biology, Hebrew University, Hadassah Medical School, Jerusalem, Israel
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29
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Abstract
Cytoplasmic RNA localization is a means to create polarity by restricting protein expression to a discrete subcellular location. RNA localization is a multistep process that begins with the recognition of cis-acting sequences within the RNA by specific trans-factors, and RNAs are localized in ribonucleoprotein (RNP) complexes that contain both the RNA and numerous protein components. Components of the localization machinery transport the RNP complex, usually in a translationally repressed state, to a distinct subcellular region, resulting in spatially restricted gene expression. Recent efforts to identify both the cis- and trans-factors required for RNA localization have elucidated RNA-protein interactions that are remodeled during localization.
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Affiliation(s)
- Raymond A Lewis
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
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30
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Munro TP, Kwon S, Schnapp BJ, St Johnston D. A repeated IMP-binding motif controls oskar mRNA translation and anchoring independently of Drosophila melanogaster IMP. ACTA ACUST UNITED AC 2006; 172:577-88. [PMID: 16476777 PMCID: PMC2063677 DOI: 10.1083/jcb.200510044] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Zip code–binding protein 1 (ZBP-1) and its Xenopus laevis homologue, Vg1 RNA and endoplasmic reticulum–associated protein (VERA)/Vg1 RNA-binding protein (RBP), bind repeated motifs in the 3′ untranslated regions (UTRs) of localized mRNAs. Although these motifs are required for RNA localization, the necessity of ZBP-1/VERA remains unresolved. We address the role of ZBP-1/VERA through analysis of the Drosophila melanogaster homologue insulin growth factor II mRNA–binding protein (IMP). Using systematic evolution of ligands by exponential enrichment, we identified the IMP-binding element (IBE) UUUAY, a motif that occurs 13 times in the oskar 3′UTR. IMP colocalizes with oskar mRNA at the oocyte posterior, and this depends on the IBEs. Furthermore, mutation of all, or subsets of, the IBEs prevents oskar mRNA translation and anchoring at the posterior. However, oocytes lacking IMP localize and translate oskar mRNA normally, illustrating that one cannot necessarily infer the function of an RBP from mutations in its binding sites. Thus, the translational activation of oskar mRNA must depend on the binding of another factor to the IBEs, and IMP may serve a different purpose, such as masking IBEs in RNAs where they occur by chance. Our findings establish a parallel requirement for IBEs in the regulation of localized maternal mRNAs in D. melanogaster and X. laevis.
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Affiliation(s)
- Trent P Munro
- The Gurdon Institute, University of Cambridge, Cambridge CB2 1QR, England, UK
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31
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Czaplinski K, Mattaj IW. 40LoVe interacts with Vg1RBP/Vera and hnRNP I in binding the Vg1-localization element. RNA (NEW YORK, N.Y.) 2006; 12:213-22. [PMID: 16373488 PMCID: PMC1370901 DOI: 10.1261/rna.2820106] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Localizing mRNAs within the cytoplasm gives cells the ability to spatially restrict protein production, a powerful means to regulate gene expression. Localized mRNA is often visible in microscopically observable particles or granules, and the association of mRNA localization with these structures is an indication that particles or granules may be essential to the localization process. Understanding how such structures form will therefore be important for understanding the function of localization RNPs (L-RNPs). We previously identified a novel component of an L-RNP from the Vg1 mRNA from Xenopus oocytes called 40LoVe. 40LoVe interaction with the Vg1-localization element (Vg1LE) was previously shown to be dependent on the VM1 and E2 sequence motifs within the Vg1LE that cross-link to hnRNP I and Vg1RBP/Vera, respectively. We report interaction of these motif-binding proteins with 40LoVe and identify a 40LoVe-Xenopus hnRNP D/AUF1 interaction. We further demonstrate that titration of VM1 and E2 motif binding activity in vivo surprisingly suggests that the motif binding proteins have differing roles during Vg1LE-dependent mRNA localization.
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32
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Horvay K, Claussen M, Katzer M, Landgrebe J, Pieler T. Xenopus Dead end mRNA is a localized maternal determinant that serves a conserved function in germ cell development. Dev Biol 2006; 291:1-11. [PMID: 16448642 DOI: 10.1016/j.ydbio.2005.06.013] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Revised: 06/06/2005] [Accepted: 06/13/2005] [Indexed: 11/15/2022]
Abstract
Germ plasm formation is considered to define the first step in germ cell development. Xenopus Dead end represents a germ plasm specific transcript that is homologous to the previously characterized zebrafish dead end, which is required for germ cell migration and survival. XDead end mRNA localizes to the vegetal pole of Xenopus oocytes; in contrast to all other known germ plasm associated transcripts in Xenopus, XDead end is transported via the late transport pathway, suggesting a different mode of germ plasm restriction. Vegetal localization in the oocyte is achieved via a localization element mapping to a 251 nucleotide element in the 3'-UTR. This RNA sequence binds to a set of proteins characteristic for the late localization pathway and to one additional protein of 38 kDa. Inhibition of XDead end translation in Xenopus embryos results in a loss of primordial germ cells at tadpole stages of development. Early specification events do not seem to be affected, but the primordial germ cells fail to migrate dorsally and eventually disappear. This phenotype is very similar to what has been observed in the zebrafish, indicating that the role of XDead end in germ cell development has been conserved in evolution.
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Affiliation(s)
- Katja Horvay
- Institut für Biochemie und Molekulare Zellbiologie, Georg-August-Universität, Justus-von-Liebig Weg 11, D-37077 Göttingen, Germany
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33
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Machado RJ, Moore W, Hames R, Houliston E, Chang P, King ML, Woodland HR. Xenopus Xpat protein is a major component of germ plasm and may function in its organisation and positioning. Dev Biol 2005; 287:289-300. [PMID: 16216237 DOI: 10.1016/j.ydbio.2005.08.044] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 08/23/2005] [Accepted: 08/26/2005] [Indexed: 01/27/2023]
Abstract
In many animals, including Drosophila, C. elegans, zebrafish and Xenopus, the germ line is specified by maternal determinants localised in a distinct cytoplasmic structure called the germ plasm. This is consists of dense granules, mitochondria, and specific localised RNAs. We have characterised the expression and properties of the protein encoded by Xpat, an RNA localised to the germ plasm of Xenopus. Immunofluorescence and immunoblotting showed that this novel protein is itself a major constituent of germ plasm throughout oogenesis and early development, although it is also present in other regions of oocytes and embryos, including their nuclei. We found that an Xpat-GFP fusion protein can localise correctly in cultured oocytes, in early oocytes to the 'mitochondrial cloud', from which germ plasm originates, and in later oocytes to the vegetal cortex. The localisation process was microtubule-dependent, while cortical anchoring required microfilaments. Xpat-GFP expressed in late stage oocytes assembled into circular fields of multi-particulate structures resembling endogenous fields of germ plasm islands. Furthermore these structures could be induced to form at ectopic sites by manipulation of culture conditions. Ectopic Xpat-GFP islands were able to recruit mitochondria, a major germ plasm component. These data suggest that Xpat protein has an important role in Xenopus germ plasm formation, positioning and maintenance.
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Affiliation(s)
- Rachel J Machado
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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34
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Minakhina S, Steward R. Axes formation and RNA localization. Curr Opin Genet Dev 2005; 15:416-21. [PMID: 15967657 DOI: 10.1016/j.gde.2005.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2005] [Accepted: 06/08/2005] [Indexed: 12/12/2022]
Abstract
Axes formation in flies and frogs largely depends on RNA localization pathways functioning in the oocytes. It is thought that motors moving along the cytoskeleton enable the selective transport of RNAs to different destinations during oocyte development. Many of the steps in RNA localization are conserved, despite the existence of a variety of mechanisms, including the formation of nuclear ribonucleoprotein complexes, and active transport along microtubules.
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Affiliation(s)
- Svetlana Minakhina
- Waksman Institute, Department of Molecular Biology and Biochemistry, NJ Cancer Center, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
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35
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Abstract
RNA-binding proteins play a major part in the control of gene expression during early development. At this stage, the majority of regulation occurs at the levels of translation and RNA localization. These processes are, in general, mediated by RNA-binding proteins interacting with specific sequence motifs in the 3'-untranslated regions of their target RNAs. Although initial work concentrated on the analysis of these sequences and their trans-acting factors, we are now beginning to gain an understanding of the mechanisms by which some of these proteins function. In this review, we will describe a number of different families of RNA-binding proteins, grouping them together on the basis of common regulatory strategies, and emphasizing the recurrent themes that occur, both across different species and as a response to different biological problems.
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36
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Czaplinski K, Köcher T, Schelder M, Segref A, Wilm M, Mattaj IW. Identification of 40LoVe, a Xenopus hnRNP D family protein involved in localizing a TGF-beta-related mRNA during oogenesis. Dev Cell 2005; 8:505-15. [PMID: 15809033 DOI: 10.1016/j.devcel.2005.01.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2004] [Revised: 01/13/2005] [Accepted: 01/19/2005] [Indexed: 01/10/2023]
Abstract
Asymmetric distribution of cellular components underlies many biological processes, and the localization of mRNAs within domains of the cytoplasm is one important mechanism of establishing and maintaining cellular asymmetry. mRNA localization often involves assembly of large ribonucleoproteins (RNPs) in the cytoplasm. Using an RNA affinity chromatography approach, we investigated localization RNP formation on the vegetal localization element (VLE) of the mRNA encoding Vg1, a Xenopus TGF-beta family member. We identified 40LoVe, an hnRNP D family protein, as a specific VLE binding protein from Xenopus oocytes. Interaction of 40LoVe with the VLE strictly correlates with the ability of the RNA to localize, and antibodies against 40LoVe inhibit vegetal localization in vivo in oocytes. Our results associate an hnRNP D protein with mRNA localization and have implications for several functions mediated by this important protein family.
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Affiliation(s)
- Kevin Czaplinski
- EMBL Gene Expression Programme, Meyerhofstrasse 1, Heidelberg 69117, Germany
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37
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Berekelya LA, Ponomarev MB, Mikryukov AA, Luchinskaya NN, Belyavsky AV. Molecular Mechanisms of Germ Line Cell Determination in Animals. Mol Biol 2005. [DOI: 10.1007/s11008-005-0073-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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38
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Abstract
mRNA localization is a common mechanism for targeting proteins to regions of the cell where they are required. It has an essential role in localizing cytoplasmic determinants, controlling the direction of protein secretion and allowing the local control of protein synthesis in neurons. New methods for in vivo labelling have revealed that several mRNAs are transported by motor proteins, but how most mRNAs are coupled to these proteins remains obscure.
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Affiliation(s)
- Daniel St Johnston
- The Gurdon Institute and The Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
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39
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Zhou Y, Zhang J, King ML. Polarized distribution of mRNAs encoding a putative LDL receptor adaptor protein, xARH (autosomal recessive hypercholesterolemia) in Xenopus oocytes. Mech Dev 2005; 121:1249-58. [PMID: 15327785 DOI: 10.1016/j.mod.2004.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Revised: 04/30/2004] [Accepted: 05/14/2004] [Indexed: 10/26/2022]
Abstract
The Xenopus homologue of hARH (human autosomal recessive hypercholesterolemia) was identified in a screen for vegetally localized RNAs. xARH contains a N-terminal phosphotyrosine binding (PTB) domain that is 91% identical to that of the human gene, a domain previously shown to bind the LDL receptor family members. Maternal xARH, unlike hARH, is present as two transcripts that differ in their 3' UTRs. The large transcript, xARH-alpha, primarily localizes to the oocyte vegetal cortex. The small transcript, xARH-beta, is not localized. During embryogenesis, xARH RNA is found redistributed in a perinuclear pattern. Similar to hARH, xARH is found in the adult liver, but at low levels compared to oocytes. Downstream of the PTB domain is a conserved clathrin box and a C terminal region 50% identical to that of hARH. Previous in vitro studies from this lab have shown xARH can bind the LDLR as well as the vitellogenin (VTG) receptor. We find that injection of the C terminal region missing the PTB domain significantly reduces the internalization of VTG in early stage oocytes, an event that requires the VTG receptor. The data strongly suggest that xARH encodes an adaptor protein that functions in the essential receptor-mediated endocytosis of nutrients during oogenesis. Because xARH protein is found uniformly distributed along the animal/vegetal axis in oocytes, we propose that the localization of xARH-alpha to the vegetal cortex while xARH-beta remains unlocalized, facilitates the uniform distribution of the protein in this extraordinarily large cell.
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Affiliation(s)
- Yi Zhou
- Department of Cell Biology and Anatomy, University of Miami School of Medicine, 1011 NW 15th St., Miami, FL 33136, USA
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40
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Choo S, Heinrich B, Betley JN, Chen Z, Deshler JO. Evidence for common machinery utilized by the early and late RNA localization pathways in Xenopus oocytes. Dev Biol 2005; 278:103-17. [PMID: 15649464 DOI: 10.1016/j.ydbio.2004.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Revised: 10/25/2004] [Accepted: 10/27/2004] [Indexed: 11/24/2022]
Abstract
In Xenopus, an early and a late pathway exist for the selective localization of RNAs to the vegetal cortex during oogenesis. Previous work has suggested that distinct cellular mechanisms mediate localization during these pathways. Here, we provide several independent lines of evidence supporting the existence of common machinery for RNA localization during the early and late pathways. Data from RNA microinjection assays show that early and late pathway RNAs compete for common localization factors in vivo, and that the same short RNA sequence motifs are required for localization during both pathways. In addition, quantitative filter binding assays demonstrate that the late localization factor Vg RBP/Vera binds specifically to several early pathway RNA localization elements. Finally, confocal imaging shows that early pathway RNAs associate with a perinuclear microtubule network that connects to the mitochondrial cloud of stage I oocytes suggesting that motor driven transport plays a role during the early pathway as it does during the late pathway. Taken together, our data indicate that common machinery functions during the early and late pathways. Thus, RNA localization to the vegetal cortex may be a regulated process such that differential interactions with basal factors determine when distinct RNAs are localized during oogenesis.
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Affiliation(s)
- Soheun Choo
- Molecular Biology and Biochemistry Program, Boston University, Boston, Massachusetts 02215, USA
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41
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Chabanon H, Nury D, Mickleburgh I, Burtle B, Hesketh J. Characterization of the cis-acting element directing perinuclear localization of the metallothionein-1 mRNA. Biochem Soc Trans 2004; 32:702-4. [PMID: 15493992 DOI: 10.1042/bst0320702] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Subcellular localization of mRNAs is a key mechanism for the synthesis of proteins close to their site of function. The mRNA encoding MT-1 (metallothionein-1) is localized in the perinuclear cytoplasm, where it is associated with cytoskeletal-bound polysomes. This localization relies on sequences present in the 3′-UTR (3′-untranslated region). The present study aims to characterize the cis-acting localization element(s) within the 3′-UTR. Using transfected cells expressing tagged MT-1 differing in their 3′-UTRs (deleted or mutated), the section(s) of this region required for directing MT-1 transcripts to the perinuclear cytoplasm has been investigated. Different 3′-UTRs were also used in UV cross-linking experiments that highlighted two distinct regions (nt 26–30 and 66–76) necessary for the binding of a protein of approx. 50 kDa, presumably involved in the mRNA targeting. The poor sequence homology between the MT-1 3′-UTR of various species, together with the bipartite nature of the required cis-element, indicates the involvement of a particular structure in the localization signal. The secondary structure of the MT-1 3′-UTR was investigated using enzymic and chemical probing. Current structural analysis of mutant 3′-UTRs will allow the critical structural features of the MT-1 mRNA perinuclear localization signal to be defined.
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Affiliation(s)
- H Chabanon
- Institute of Cellular and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
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Chang P, Torres J, Lewis RA, Mowry KL, Houliston E, King ML. Localization of RNAs to the mitochondrial cloud in Xenopus oocytes through entrapment and association with endoplasmic reticulum. Mol Biol Cell 2004; 15:4669-81. [PMID: 15292452 PMCID: PMC519158 DOI: 10.1091/mbc.e04-03-0265] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The germ cell lineage in Xenopus is specified by the inheritance of germ plasm, which originates within a distinct "mitochondrial cloud" (MC) in previtellogenic oocytes. Germ plasm contains localized RNAs implicated in germ cell development, including Xcat2 and Xdazl. To understand the mechanism of the early pathway through which RNAs localize to the MC, we applied live confocal imaging and photobleaching analysis to oocytes microinjected with fluorescent Xcat2 and Xdazl RNA constructs. These RNAs dispersed evenly throughout the cytoplasm through diffusion and then became progressively immobilized and formed aggregates in the MC. Entrapment in the MC was not prevented by microtubule disruption and did not require localization to germinal granules. Immobilized RNA constructs codistributed and showed coordinated movement with densely packed endoplasmic reticulum (ER) concentrated in the MC, as revealed with Dil16(3) labeling and immunofluorescence analysis. Vg1RBP/Vera protein, which has been implicated in linking late pathway RNAs to vegetal ER, was shown to bind specifically both wild-type Xcat2 3' untranslated region and localization-defective constructs. We found endogenous Vg1RBP/Vera and Vg1RBP/Vera-green fluorescent protein to be largely excluded from the MC but subsequently to codistribute with Xcat2 and ER at the vegetal cortex. We conclude that germ line RNAs localize into the MC through a diffusion/entrapment mechanism involving Vg1RBP/Vera-independent association with ER.
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Affiliation(s)
- Patrick Chang
- Unité Mixte de Recherche 7009 Centre National pour la Recherche Scientifique/Université Pierre et Marie Curie, Observatoire Océanologique, 06230 Villefranche sur Mer, France
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Abstract
Cytoplasmic localization of mRNAs is a widespread mechanism for generating cell polarity and can provide the basis for patterning during embryonic development. A prominent example of this is localization of maternal mRNAs in Xenopus oocytes, a process requiring recognition of essential RNA sequences by protein components of the localization machinery. However, it is not yet clear how and when such protein factors associate with localized RNAs to carry out RNA transport. To trace the RNA-protein interactions that mediate RNA localization, we analyzed RNP complexes from the nucleus and cytoplasm. We find that an early step in the localization pathway is recognition of localized RNAs by specific RNA-binding proteins in the nucleus. After transport into the cytoplasm, the RNP complex is remodeled and additional transport factors are recruited. These results suggest that cytoplasmic RNA localization initiates in the nucleus and that binding of specific RNA-binding proteins in the nucleus may act to target RNAs to their appropriate destinations in the cytoplasm.
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Affiliation(s)
- Tracy L Kress
- Box G-J2, Brown University, Providence, RI 02912, USA
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