1
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Milano SN, Bayer LV, Ko JJ, Casella CE, Bratu DP. The role of ER exit sites in maintaining P-body organization and transmitting ER stress response during Drosophila melanogaster oogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601952. [PMID: 39005311 PMCID: PMC11245038 DOI: 10.1101/2024.07.03.601952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Processing bodies (P-bodies) are cytoplasmic membrane-less organelles which host multiple mRNA processing events. While the fundamental principles of P-body organization are beginning to be elucidated in vitro, a nuanced understanding of how their assembly is regulated in vivo remains elusive. Here, we investigate the potential link between ER exit sites and P-bodies in Drosophila melanogaster egg chambers. Employing a combination of live and super-resolution imaging, we found that P-bodies associated with ER exit sites are larger and less mobile than cytoplasmic P-bodies, indicating that they constitute a distinct class of P-bodies which are more mature than their cytoplasmic counterparts. Moreover, we demonstrate that altering the composition of ER exit sites has differential effects on core P-body proteins (Me31B, Cup, and Trailer Hitch) suggesting a potential role for ER exit sites in P-body organization. We further show that in the absence of ER exit sites, P-body integrity is compromised and the stability and translational repression efficiency of the maternal mRNA, oskar, are reduced. Finally, we show that ER stress is communicated to P-bodies via ER exit sites, highlighting the pivotal role of ER exit sites as a bridge between membrane-bound and membrane-less organelles in ER stress response. Together, our data unveils the significance of ER exit sites not only in governing P-body organization, but also in facilitating inter-organellar communication during stress, potentially bearing implications for a variety of disease pathologies.
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Affiliation(s)
- Samantha N. Milano
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, NY, 10016 USA
| | - Livia V. Bayer
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
| | - Julie J. Ko
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
| | - Caroline E. Casella
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
| | - Diana P. Bratu
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, NY, 10016 USA
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2
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Kara E, McCambridge A, Proffer M, Dilts C, Pumnea B, Eshak J, Smith KA, Fielder I, Doyle DA, Ortega BM, Mukatash Y, Malik N, Mohammed AR, Govani D, Niepielko MG, Gao M. Mutational analysis of the functional motifs of the DEAD-box RNA helicase Me31B/DDX6 in Drosophila germline development. FEBS Lett 2023; 597:1848-1867. [PMID: 37235728 PMCID: PMC10389067 DOI: 10.1002/1873-3468.14668] [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: 01/30/2023] [Revised: 04/24/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023]
Abstract
Me31B/DDX6 is a DEAD-box family RNA helicase playing roles in post-transcriptional RNA regulation in different cell types and species. Despite the known motifs/domains of Me31B, the in vivo functions of the motifs remain unclear. Here, we used the Drosophila germline as a model and used CRISPR to mutate the key Me31B motifs/domains: helicase domain, N-terminal domain, C-terminal domain and FDF-binding motif. Then, we performed screening characterization on the mutants and report the effects of the mutations on the Drosophila germline, on processes such as fertility, oogenesis, embryo patterning, germline mRNA regulation and Me31B protein expression. The study indicates that the Me31B motifs contribute different functions to the protein and are needed for proper germline development, providing insights into the in vivo working mechanism of the helicase.
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Affiliation(s)
- Evan Kara
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | | | - Megan Proffer
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Carol Dilts
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Brooke Pumnea
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - John Eshak
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Korey A. Smith
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Isaac Fielder
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Dominique A. Doyle
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Bianca M. Ortega
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Yousif Mukatash
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Noor Malik
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | | | - Deep Govani
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Matthew G. Niepielko
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
- Biology Department, Kean University, Union, NJ, USA
| | - Ming Gao
- Biology Department, Indiana University Northwest, Gary, IN, USA
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3
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Rothé B, Fortier S, Gagnieux C, Schmuziger C, Constam DB. Antagonistic interactions among structured domains in the multivalent Bicc1-ANKS3-ANKS6 protein network govern phase transitioning of target mRNAs. iScience 2023; 26:106855. [PMID: 37275520 PMCID: PMC10232731 DOI: 10.1016/j.isci.2023.106855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 06/07/2023] Open
Abstract
The growing number of diseases linked to aberrant phase transitioning of ribonucleoproteins highlights the need to uncover how the interplay between multivalent protein and RNA interactions is regulated. Cytoplasmic granules of the RNA binding protein Bicaudal-C (Bicc1) are regulated by the ciliopathy proteins ankyrin (ANK) and sterile alpha motif (SAM) domain-containing ANKS3 and ANKS6, but whether and how target mRNAs are affected is unknown. Here, we show that head-to-tail polymers of Bicc1 nucleated by its SAM domain are interconnected by K homology (KH) domains in a protein meshwork that mediates liquid-to-gel transitioning of client transcripts. Moreover, while the dispersion of these granules by ANKS3 concomitantly released bound mRNAs, co-recruitment of ANKS6 by ANKS3 reinstated Bicc1 condensation and ribonucleoparticle assembly. RNA-independent Bicc1 polymerization and its dual regulation by ANKS3 and ANKS6 represent a new mechanism to couple the reversible immobilization of client mRNAs to controlled protein phase transitioning between distinct metastable states.
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Affiliation(s)
- Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Simon Fortier
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Céline Gagnieux
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Céline Schmuziger
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Daniel B. Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
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4
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Layana C, Vilardo ES, Corujo G, Hernández G, Rivera-Pomar R. Drosophila Me31B is a Dual eIF4E-Interacting Protein. J Mol Biol 2023; 435:167949. [PMID: 36638908 DOI: 10.1016/j.jmb.2023.167949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Eukaryotic translation initiation factor 4E (eIF4E) is a key factor involved in different aspects of mRNA metabolism. Drosophila melanogaster genome encodes eight eIF4E isoforms, and the canonical isoform eIF4E-1 is a ubiquitous protein that plays a key role in mRNA translation. eIF4E-3 is specifically expressed in testis and controls translation during spermatogenesis. In eukaryotic cells, translational control and mRNA decay is highly regulated in different cytoplasmic ribonucleoprotein foci, which include the processing bodies (PBs). In this study, we show that Drosophila eIF4E-1 and eIF4E-3 occur in PBs along the DEAD-box RNA helicase Me31B. We show that Me31B interacts with eIF4E-1 and eIF4E-3 by means of yeast two-hybrid system, FRET in D. melanogaster S2 cells and coimmunoprecipitation in testis. Truncation and point mutations of Me31B proteins show two eIF4E-binding sites located in different protein domains. Residues Y401-L407 (at the carboxy-terminus) are essential for interaction with eIF4E-1, whereas residues F63-L70 (at the amino-terminus) are critical for interaction with eIF4E-3. The residue W117 in eIF4E-1 and the homolog position F103 in eIF4E-3 are necessary for Me31B-eIF4E interaction suggesting that the change of tryptophan to phenylalanine provides specificity. Me31B represents a novel type of eIF4E-interacting protein with dual and specific interaction domains that might be recognized by different eIF4E isoforms in different tissues, adding complexity to the control of gene expression in eukaryotes.
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Affiliation(s)
- Carla Layana
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Boulevard 120 N° 1459, 1900 La Plata, Argentina.
| | - Emiliano Salvador Vilardo
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Boulevard 120 N° 1459, 1900 La Plata, Argentina
| | - Gonzalo Corujo
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Boulevard 120 N° 1459, 1900 La Plata, Argentina
| | - Greco Hernández
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (Instituto Nacional de Cancerología, INCan), 22 San Fernando Ave., Tlalpan, 14080 Mexico City, Mexico
| | - Rolando Rivera-Pomar
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Boulevard 120 N° 1459, 1900 La Plata, Argentina; Centro de Investigación y Transferencia del Noroeste de Buenos Aires (CITNOBA) - Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Av. Presidente Frondizi Km 4, 2700 Pergamino, Argentina; Molecular Developmental Biology Emeritus Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
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5
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Jensen L, Venkei ZG, Watase GJ, Bisai B, Pletcher S, Lee CY, Yamashita YM. me31B regulates stem cell homeostasis by preventing excess dedifferentiation in the Drosophila male germline. J Cell Sci 2021; 134:269264. [PMID: 34164657 PMCID: PMC8325955 DOI: 10.1242/jcs.258757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/14/2021] [Indexed: 12/31/2022] Open
Abstract
Tissue-specific stem cells maintain tissue homeostasis by providing a continuous supply of differentiated cells throughout the life of organisms. Differentiated/differentiating cells can revert back to a stem cell identity via dedifferentiation to help maintain the stem cell pool beyond the lifetime of individual stem cells. Although dedifferentiation is important for maintaining the stem cell population, it is speculated that it underlies tumorigenesis. Therefore, this process must be tightly controlled. Here, we show that a translational regulator, me31B, plays a critical role in preventing excess dedifferentiation in the Drosophila male germline: in the absence of me31B, spermatogonia dedifferentiate into germline stem cells (GSCs) at a dramatically elevated frequency. Our results show that the excess dedifferentiation is likely due to misregulation of nos, a key regulator of germ cell identity and GSC maintenance. Taken together, our data reveal negative regulation of dedifferentiation to balance stem cell maintenance with differentiation.
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Affiliation(s)
- Lindy Jensen
- Life Sciences Institute, Department of Molecular and Integrative Physiology, University of Michigan Ann Arbor, MI 48109, USA
| | - Zsolt G Venkei
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Department of Biology, Cambridge, MA 02142, USA
| | - George J Watase
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Department of Biology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Cambridge, MA 02142, USA
| | - Bitarka Bisai
- Life Sciences Institute, Department of Molecular and Integrative Physiology, University of Michigan Ann Arbor, MI 48109, USA
| | - Scott Pletcher
- Life Sciences Institute, Department of Molecular and Integrative Physiology, University of Michigan Ann Arbor, MI 48109, USA
| | - Cheng-Yu Lee
- Life Sciences Institute, Department of Molecular and Integrative Physiology, University of Michigan Ann Arbor, MI 48109, USA
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Department of Biology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Cambridge, MA 02142, USA
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6
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Avilés-Pagán EE, Hara M, Orr-Weaver TL. The GNU subunit of PNG kinase, the developmental regulator of mRNA translation, binds BIC-C to localize to RNP granules. eLife 2021; 10:67294. [PMID: 34250903 PMCID: PMC8313231 DOI: 10.7554/elife.67294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/09/2021] [Indexed: 11/15/2022] Open
Abstract
Control of mRNA translation is a key mechanism by which the differentiated oocyte transitions to a totipotent embryo. In Drosophila, the PNG kinase complex regulates maternal mRNA translation at the oocyte-to-embryo transition. We previously showed that the GNU activating subunit is crucial in regulating PNG and timing its activity to the window between egg activation and early embryogenesis (Hara et al., 2017). In this study, we find associations between GNU and proteins of RNP granules and demonstrate that GNU localizes to cytoplasmic RNP granules in the mature oocyte, identifying GNU as a new component of a subset of RNP granules. Furthermore, we define roles for the domains of GNU. Interactions between GNU and the granule component BIC-C reveal potential conserved functions for translational regulation in metazoan development. We propose that by binding to BIC-C, upon egg activation GNU brings PNG to its initial targets, translational repressors in RNP granules.
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Affiliation(s)
- Emir E Avilés-Pagán
- Department of Biology, MIT, Cambridge, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Masatoshi Hara
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Terry L Orr-Weaver
- Department of Biology, MIT, Cambridge, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States
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7
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Comparative Proteomics Reveal Me31B's Interactome Dynamics, Expression Regulation, and Assembly Mechanism into Germ Granules during Drosophila Germline Development. Sci Rep 2020; 10:564. [PMID: 31953495 PMCID: PMC6969142 DOI: 10.1038/s41598-020-57492-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 12/26/2019] [Indexed: 01/23/2023] Open
Abstract
Me31B is a protein component of Drosophila germ granules and plays an important role in germline development by interacting with other proteins and RNAs. To understand the dynamic changes that the Me31B interactome undergoes from oogenesis to early embryogenesis, we characterized the early embryo Me31B interactome and compared it to the known ovary interactome. The two interactomes shared RNA regulation proteins, glycolytic enzymes, and cytoskeleton/motor proteins, but the core germ plasm proteins Vas, Tud, and Aub were significantly decreased in the embryo interactome. Our follow-up on two RNA regulations proteins present in both interactomes, Tral and Cup, revealed that they colocalize with Me31B in nuage granules, P-bodies/sponge bodies, and possibly in germ plasm granules. We further show that Tral and Cup are both needed for maintaining Me31B protein level and mRNA stability, with Tral’s effect being more specific. In addition, we provide evidence that Me31B likely colocalizes and interacts with germ plasm marker Vas in the ovaries and early embryo germ granules. Finally, we show that Me31B’s localization in germ plasm is likely independent of the Osk-Vas-Tud-Aub germ plasm assembly pathway although its proper enrichment in the germ plasm may still rely on certain conserved germ plasm proteins.
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8
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Rothé B, Gagnieux C, Leal-Esteban LC, Constam DB. Role of the RNA-binding protein Bicaudal-C1 and interacting factors in cystic kidney diseases. Cell Signal 2019; 68:109499. [PMID: 31838063 DOI: 10.1016/j.cellsig.2019.109499] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 01/03/2023]
Abstract
Polycystic kidneys frequently associate with mutations in individual components of cilia, basal bodies or centriolar satellites that perturb complex protein networks. In this review, we focus on the RNA-binding protein Bicaudal-C1 (BICC1) which was found mutated in renal cystic dysplasia, and on its interactions with the ankyrin repeat and sterile α motif (SAM)-containing proteins ANKS3 and ANKS6 and associated kinases and their partially overlapping ciliopathy phenotypes. After reviewing BICC1 homologs in model organisms and their functions in mRNA and cell metabolism during development and in renal tubules, we discuss recent insights from cell-based assays and from structure analysis of the SAM domains, and how SAM domain oligomerization might influence multivalent higher order complexes that are implicated in ciliary signal transduction.
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Affiliation(s)
- Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland
| | - Céline Gagnieux
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland
| | - Lucia Carolina Leal-Esteban
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland; Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Daniel B Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland.
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9
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Leal-Esteban LC, Rothé B, Fortier S, Isenschmid M, Constam DB. Role of Bicaudal C1 in renal gluconeogenesis and its novel interaction with the CTLH complex. PLoS Genet 2018; 14:e1007487. [PMID: 29995892 PMCID: PMC6056059 DOI: 10.1371/journal.pgen.1007487] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/23/2018] [Accepted: 06/13/2018] [Indexed: 01/06/2023] Open
Abstract
Altered glucose and lipid metabolism fuel cystic growth in polycystic kidneys, but the cause of these perturbations is unclear. Renal cysts also associate with mutations in Bicaudal C1 (Bicc1) or in its self-polymerizing sterile alpha motif (SAM). Here, we found that Bicc1 maintains normoglycemia and the expression of the gluconeogenic enzymes FBP1 and PEPCK in kidneys. A proteomic screen revealed that Bicc1 interacts with the C-Terminal to Lis-Homology domain (CTLH) complex. Since the orthologous Gid complex in S. cerevisae targets FBP1 and PEPCK for degradation, we mapped the topology among CTLH subunits and found that SAM-mediated binding controls Bicc1 protein levels, whereas Bicc1 inhibited the accumulation of several CTLH subunits. Under the conditions analyzed, Bicc1 increased FBP1 protein levels independently of the CTLH complex. Besides linking Bicc1 to cell metabolism, our findings reveal new layers of complexity in the regulation of renal gluconeogenesis compared to lower eukaryotes. Polycystic kidney diseases (PKD) are incurable inherited chronic disorders marked by fluid-filled cysts that frequently cause renal failure. A glycolytic metabolism reminiscent of cancerous cells accelerates cystic growth, but the mechanism underlying such metabolic re-wiring is poorly understood. PKD-like cystic kidneys also develop in mice that lack the RNA-binding protein Bicaudal-C (Bicc1), and mutations in a single copy of human BICC1 associate with renal cystic dysplasia. Here, we report that Bicc1 regulates renal gluconeogenesis. A screen for interacting factors revealed that Bicc1 binds the C-Terminal to Lis-Homology domain (CTLH) complex, which in lower eukaryotes mediates degradation of gluconeogenic enzymes. By contrast, Bicc1 and the mammalian CTLH complex regulated each other, and Bicc1 stimulated the accumulation of the rate-limiting gluconeogenic enzyme even in cells depleted of CTLH subunits. Our finding that Bicc1 is required for normoglycemia implies that renal gluconeogenesis may be important to inhibit cyst formation.
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Affiliation(s)
- Lucia Carolina Leal-Esteban
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Simon Fortier
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Manuela Isenschmid
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Daniel B. Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- * E-mail:
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10
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Modeling Renal Disease "On the Fly". BIOMED RESEARCH INTERNATIONAL 2018; 2018:5697436. [PMID: 29955604 PMCID: PMC6000847 DOI: 10.1155/2018/5697436] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 04/17/2018] [Indexed: 12/22/2022]
Abstract
Detoxification is a fundamental function for all living organisms that need to excrete catabolites and toxins to maintain homeostasis. Kidneys are major organs of detoxification that maintain water and electrolyte balance to preserve physiological functions of vertebrates. In insects, the renal function is carried out by Malpighian tubules and nephrocytes. Due to differences in their circulation, the renal systems of mammalians and insects differ in their functional modalities, yet carry out similar biochemical and physiological functions and share extensive genetic and molecular similarities. Evolutionary conservation can be leveraged to model specific aspects of the complex mammalian kidney function in the genetic powerhouse Drosophila melanogaster to study how genes interact in diseased states. Here, we compare the human and Drosophila renal systems and present selected fly disease models.
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11
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Roy D, Rajyaguru PI. Suppressor of clathrin deficiency (Scd6)-An emerging RGG-motif translation repressor. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1479. [DOI: 10.1002/wrna.1479] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Debadrita Roy
- Department of Biochemistry; Indian Institute of Science; Bangalore India
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12
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Hara M, Lourido S, Petrova B, Lou HJ, Von Stetina JR, Kashevsky H, Turk BE, Orr-Weaver TL. Identification of PNG kinase substrates uncovers interactions with the translational repressor TRAL in the oocyte-to-embryo transition. eLife 2018; 7:33150. [PMID: 29480805 PMCID: PMC5826265 DOI: 10.7554/elife.33150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/12/2018] [Indexed: 12/19/2022] Open
Abstract
The Drosophila Pan Gu (PNG) kinase complex regulates hundreds of maternal mRNAs that become translationally repressed or activated as the oocyte transitions to an embryo. In a previous paper (Hara et al., 2017), we demonstrated PNG activity is under tight developmental control and restricted to this transition. Here, examination of PNG specificity showed it to be a Thr-kinase yet lacking a clear phosphorylation site consensus sequence. An unbiased biochemical screen for PNG substrates identified the conserved translational repressor Trailer Hitch (TRAL). Phosphomimetic mutation of the PNG phospho-sites in TRAL reduced its ability to inhibit translation in vitro. In vivo, mutation of tral dominantly suppressed png mutants and restored Cyclin B protein levels. The repressor Pumilio (PUM) has the same relationship with PNG, and we also show that PUM is a PNG substrate. Furthermore, PNG can phosphorylate BICC and ME31B, repressors that bind TRAL in cytoplasmic RNPs. Therefore, PNG likely promotes translation at the oocyte-to-embryo transition by phosphorylating and inactivating translational repressors.
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Affiliation(s)
| | | | | | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | | | | | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | - Terry L Orr-Weaver
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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13
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DeHaan H, McCambridge A, Armstrong B, Cruse C, Solanki D, Trinidad JC, Arkov AL, Gao M. An in vivo proteomic analysis of the Me31B interactome in Drosophila germ granules. FEBS Lett 2017; 591:3536-3547. [PMID: 28945271 DOI: 10.1002/1873-3468.12854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/07/2017] [Accepted: 09/15/2017] [Indexed: 12/11/2022]
Abstract
Drosophila Me31B is a conserved protein of germ granules, ribonucleoprotein complexes essential for germ cell development. Me31B post-transcriptionally regulates mRNAs by interacting with other germ granule proteins. However, a Me31B interactome is lacking. Here, we use an in vivo proteomics approach to show that the Me31B interactome contains polypeptides from four functional groups: RNA regulatory proteins, glycolytic enzymes, cytoskeleton/motor proteins, and germ plasm components. We further show that Me31B likely colocalizes with the germ plasm components Tudor (Tud), Vasa, and Aubergine in the nuage and germ plasm and provide evidence that Me31B may directly bind to Tud in a symmetrically dimethylated arginine-dependent manner. Our study supports the role of Me31B in RNA regulation and suggests its novel roles in germ granule assembly and function.
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Affiliation(s)
- Hunter DeHaan
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | | | | | - Carlie Cruse
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Dhruv Solanki
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | | | - Alexey L Arkov
- Department of Biological Sciences, Murray State University, Murray, KY, USA
| | - Ming Gao
- Biology Department, Indiana University Northwest, Gary, IN, USA
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14
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Aguilera-Gomez A, Rabouille C. Membrane-bound organelles versus membrane-less compartments and their control of anabolic pathways in Drosophila. Dev Biol 2017; 428:310-317. [PMID: 28377034 DOI: 10.1016/j.ydbio.2017.03.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 12/29/2022]
Abstract
Classically, we think of cell compartmentalization as being achieved by membrane-bound organelles. It has nevertheless emerged that membrane-less assemblies also largely contribute to this compartmentalization. Here, we compare the characteristics of both types of compartmentalization in term of maintenance of functional identities. Furthermore, membrane less-compartments are critical for sustaining developmental and cell biological events as they control major metabolic pathways. We describe two examples related to this issue in Drosophila, the role of P-bodies in the translational control of gurken in the Drosophila oocyte, and the formation of Sec bodies upon amino-acid starvation in Drosophila cells.
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Affiliation(s)
| | - Catherine Rabouille
- Hubrecht Institute of the KNAW & UMC Utrecht, 3584 CT Utrecht, The Netherlands; Department of Cell Biology, UMC Utrecht, The Netherlands; Department of Cell Biology, UMC Groningen, The Netherlands.
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15
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Li F, Ye Z, Zhai Y, Gong B, Jiang L, Wu H, Lin Y, Wan L, Yang Z, Shi Y, Wu Z. Evaluation of genome-wide susceptibility loci for high myopia in a Han Chinese population. Ophthalmic Genet 2017; 38:330-334. [PMID: 28085524 DOI: 10.1080/13816810.2016.1227455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Fang Li
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Department of Ophthalmology, Sichuan Provincial People’s Hospital, Chengdu, Sichuan, China
| | - Zimeng Ye
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- College of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Yaru Zhai
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Bo Gong
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, Sichuan, China
| | - Lingxi Jiang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Haiyan Wu
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ying Lin
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, Sichuan, China
| | - Ling Wan
- Department of Ophthalmology, Sichuan Provincial People’s Hospital, Chengdu, Sichuan, China
| | - Zhenglin Yang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, Sichuan, China
| | - Yi Shi
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, Sichuan, China
| | - Zhengzheng Wu
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Department of Ophthalmology, Sichuan Provincial People’s Hospital, Chengdu, Sichuan, China
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16
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Zfrp8 forms a complex with fragile-X mental retardation protein and regulates its localization and function. Dev Biol 2016; 410:202-212. [PMID: 26772998 DOI: 10.1016/j.ydbio.2015.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 11/13/2015] [Accepted: 12/09/2015] [Indexed: 11/21/2022]
Abstract
Fragile-X syndrome is the most commonly inherited cause of autism and mental disabilities. The Fmr1 (Fragile-X Mental Retardation 1) gene is essential in humans and Drosophila for the maintenance of neural stem cells, and Fmr1 loss results in neurological and reproductive developmental defects in humans and flies. FMRP (Fragile-X Mental Retardation Protein) is a nucleo-cytoplasmic shuttling protein, involved in mRNA silencing and translational repression. Both Zfrp8 and Fmr1 have essential functions in the Drosophila ovary. In this study, we identified FMRP, Nufip (Nuclear Fragile-X Mental Retardation Protein-interacting Protein) and Tral (Trailer Hitch) as components of a Zfrp8 protein complex. We show that Zfrp8 is required in the nucleus, and controls localization of FMRP in the cytoplasm. In addition, we demonstrate that Zfrp8 genetically interacts with Fmr1 and tral in an antagonistic manner. Zfrp8 and FMRP both control heterochromatin packaging, also in opposite ways. We propose that Zfrp8 functions as a chaperone, controlling protein complexes involved in RNA processing in the nucleus.
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17
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Abstract
Loss of the RNA-binding protein Bicaudal-C (Bicc1) provokes renal and pancreatic cysts as well as ectopic Wnt/β-catenin signaling during visceral left-right patterning. Renal cysts are linked to defective silencing of Bicc1 target mRNAs, including adenylate cyclase 6 (AC6). RNA binding of Bicc1 is mediated by N-terminal KH domains, whereas a C-terminal sterile alpha motif (SAM) self-polymerizes in vitro and localizes Bicc1 in cytoplasmic foci in vivo. To assess a role for multimerization in silencing, we conducted structure modeling and then mutated the SAM domain residues which in this model were predicted to polymerize Bicc1 in a left-handed helix. We show that a SAM-SAM interface concentrates Bicc1 in cytoplasmic clusters to specifically localize and silence bound mRNA. In addition, defective polymerization decreases Bicc1 stability and thus indirectly attenuates inhibition of Dishevelled 2 in the Wnt/β-catenin pathway. Importantly, aberrant C-terminal extension of the SAM domain in bpk mutant Bicc1 phenocopied these defects. We conclude that polymerization is a novel disease-relevant mechanism both to stabilize Bicc1 and to present associated mRNAs in specific silencing platforms.
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Williams LS, Ganguly S, Loiseau P, Ng BF, Palacios IM. The auto-inhibitory domain and ATP-independent microtubule-binding region of Kinesin heavy chain are major functional domains for transport in the Drosophila germline. Development 2013; 141:176-86. [PMID: 24257625 PMCID: PMC3865757 DOI: 10.1242/dev.097592] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The major motor Kinesin-1 provides a key pathway for cell polarization through intracellular transport. Little is known about how Kinesin works in complex cellular surroundings. Several cargos associate with Kinesin via Kinesin light chain (KLC). However, KLC is not required for all Kinesin transport. A putative cargo-binding domain was identified in the C-terminal tail of fungal Kinesin heavy chain (KHC). The tail is conserved in animal KHCs and might therefore represent an alternative KLC-independent cargo-interacting region. By comprehensive functional analysis of the tail during Drosophila oogenesis we have gained an understanding of how KHC achieves specificity in its transport and how it is regulated. This is, to our knowledge, the first in vivo structural/functional analysis of the tail in animal Kinesins. We show that the tail is essential for all functions of KHC except Dynein transport, which is KLC dependent. These tail-dependent KHC activities can be functionally separated from one another by further characterizing domains within the tail. In particular, our data show the following. First, KHC is temporally regulated during oogenesis. Second, the IAK domain has an essential role distinct from its auto-inhibitory function. Third, lack of auto-inhibition in itself is not necessarily detrimental to KHC function. Finally, the ATP-independent microtubule-binding motif is required for cargo localization. These results stress that two unexpected highly conserved domains, namely the auto-inhibitory IAK and the auxiliary microtubule-binding motifs, are crucial for transport by Kinesin-1 and that, although not all cargos are conserved, their transport involves the most conserved domains of animal KHCs.
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Affiliation(s)
- Lucy S Williams
- University of Cambridge, Zoology Department, Downing Street, Cambridge CB2 3EJ, UK
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19
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Drosophila oocyte polarity and cytoskeleton organization require regulation of Ik2 activity by Spn-F and Javelin-like. Mol Cell Biol 2013; 33:4371-80. [PMID: 24019068 DOI: 10.1128/mcb.00713-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The Drosophila melanogaster Spn-F, Ik2, and Javelin-like (Jvl) proteins interact to regulate oocyte mRNA localization and cytoskeleton organization. However, the mechanism by which these proteins interact remains unclear. Using antibodies to activated Ik2, we showed that this protein is found at the region of oocyte and follicle cell where microtubule minus ends are enriched. We demonstrate that germ line Ik2 activation is diminished both in jvl and in spn-F mutant ovaries. Structure-function analysis of Spn-F revealed that the C-terminal end is critical for protein function, since it alone was able to rescue spn-F sterility. On the other hand, germ line expression of Spn-F lacking its conserved C-terminal region (Spn-FΔC) phenocopied ik2, leading to production of ventralized eggshell and bicaudal embryos. In Spn-FΔC-expressing oocytes, Gurken protein is mislocalized and oskar mRNA and protein localization is disrupted. Expression of Ik2 rescued Spn-FΔC ovarian phenotypes. We found that whereas Spn-F physically interacts with Ik2 and Jvl, Spn-FΔC physically interacts with Ik2 but not with Jvl. Thus, expression of Spn-FΔC, which lacks the Jvl-interacting domain, probably interferes with interaction of Ik2 and Jvl. In summary, our results demonstrate that Spn-F mediates the interaction between Ik2 and Jvl to control Ik2 activity.
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20
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McDermott SM, Davis I. Drosophila Hephaestus/polypyrimidine tract binding protein is required for dorso-ventral patterning and regulation of signalling between the germline and soma. PLoS One 2013; 8:e69978. [PMID: 23894566 PMCID: PMC3720928 DOI: 10.1371/journal.pone.0069978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/14/2013] [Indexed: 02/05/2023] Open
Abstract
In the Drosophila oocyte, gurken (grk) mRNA encodes a secreted TGF-α signal that specifies the future embryonic dorso-ventral axes by altering the fate of the surrounding epithelial follicle cells. We previously identified a number of RNA binding proteins that associate specifically with the 64 nucleotide grk localization signal, including the Drosophila orthologue of polypyrimidine tract-binding protein (PTB), Hephaestus (Heph). To test whether Heph is required for correct grk mRNA or protein function, we used immunoprecipitation to validate the association of Heph with grk mRNA and characterized the heph mutant phenotype. We found that Heph is a component of grk mRNP complexes but heph germline clones show that Heph is not required for grk mRNA localization. Instead, we identify a novel function for Heph in the germline and show that it is required for proper Grk protein localization. Furthermore, we show that Heph is required in the oocyte for the correct organization of the actin cytoskeleton and dorsal appendage morphogenesis. Our results highlight a requirement for an mRNA binding protein in the localization of Grk protein, which is independent of mRNA localization, and we propose that Heph is required in the germline for efficient Grk signalling to the somatic follicle cells during dorso-ventral patterning.
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Affiliation(s)
- Suzanne M. McDermott
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail: (SMM); (ID)
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail: (SMM); (ID)
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21
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Piazzon N, Maisonneuve C, Guilleret I, Rotman S, Constam DB. Bicc1 links the regulation of cAMP signaling in polycystic kidneys to microRNA-induced gene silencing. J Mol Cell Biol 2012; 4:398-408. [PMID: 22641646 DOI: 10.1093/jmcb/mjs027] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genetic defects in autosomal-dominant polycystic kidney disease (ADPKD) promote cystic growth of renal tubules, at least in part by stimulating the accumulation of cAMP. How renal cAMP levels are regulated is incompletely understood. We show that cAMP and the expression of its synthetic enzyme adenylate cyclase-6 (AC6) are up-regulated in cystic kidneys of Bicc1(-)(/-) knockout mice. Bicc1, a protein comprising three K homology (KH) domains and a sterile alpha motif (SAM), is expressed in proximal tubules. The KH domains independently bind AC6 mRNA and recruit the miR-125a from Dicer, whereas the SAM domain enables silencing by Argonaute and TNRC6A/GW182. Bicc1 similarly induces silencing of the protein kinase inhibitor PKIα by miR-27a. Thus, Bicc1 is needed on these target mRNAs for silencing by specific miRNAs. The repression of AC6 by Bicc1 might explain why cysts in ADPKD patients preferentially arise from distal tubules.
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Affiliation(s)
- Nathalie Piazzon
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland
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22
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The Bic-C family of developmental translational regulators. Comp Funct Genomics 2012; 2012:141386. [PMID: 22611335 PMCID: PMC3352585 DOI: 10.1155/2012/141386] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 02/18/2012] [Indexed: 12/14/2022] Open
Abstract
Regulation of mRNA translation is especially important during cellular and developmental processes. Many evolutionarily conserved proteins act in the context of multiprotein complexes and modulate protein translation both at the spatial and the temporal levels. Among these, Bicaudal C constitutes a family of RNA binding proteins whose founding member was first identified in Drosophila and contains orthologs in vertebrates. We discuss recent advances towards understanding the functions of these proteins in the context of the cellular and developmental biology of many model organisms and their connection to human disease.
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23
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McDermott SM, Meignin C, Rappsilber J, Davis I. Drosophila Syncrip binds the gurken mRNA localisation signal and regulates localised transcripts during axis specification. Biol Open 2012; 1:488-97. [PMID: 23213441 PMCID: PMC3507208 DOI: 10.1242/bio.2012885] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In the Drosophila oocyte, mRNA transport and localised translation play a fundamental role in axis determination and germline formation of the future embryo. gurken mRNA encodes a secreted TGF-α signal that specifies dorsal structures, and is localised to the dorso-anterior corner of the oocyte via a cis-acting 64 nucleotide gurken localisation signal. Using GRNA chromatography, we characterised the biochemical composition of the ribonucleoprotein complexes that form around the gurken mRNA localisation signal in the oocyte. We identified a number of the factors already known to be involved in gurken localisation and translational regulation, such as Squid and Imp, in addition to a number of factors with known links to mRNA localisation, such as Me31B and Exu. We also identified previously uncharacterised Drosophila proteins, including the fly homologue of mammalian SYNCRIP/hnRNPQ, a component of RNA transport granules in the dendrites of mammalian hippocampal neurons. We show that Drosophila Syncrip binds specifically to gurken and oskar, but not bicoid transcripts. The loss-of-function and overexpression phenotypes of syncrip in Drosophila egg chambers show that the protein is required for correct grk and osk mRNA localisation and translational regulation. We conclude that Drosophila Syncrip is a new factor required for localisation and translational regulation of oskar and gurken mRNA in the oocyte. We propose that Syncrip/SYNCRIP is part of a conserved complex associated with localised transcripts and required for their correct translational regulation in flies and mammals.
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Affiliation(s)
- Suzanne M McDermott
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU , UK ; Present address: Seattle Biomedical Research Institute, 307 Westlake Avenue N, Suite 500, Seattle, WA 98109-5219, USA
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24
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Koepke J, Kaffarnik F, Haag C, Zarnack K, Luscombe NM, König J, Ule J, Kellner R, Begerow D, Feldbrügge M. The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1. Mol Cell Proteomics 2011; 10:M111.011213. [PMID: 21808052 DOI: 10.1074/mcp.m111.011213] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Long-distance transport of mRNAs is crucial in determining spatio-temporal gene expression in eukaryotes. The RNA-binding protein Rrm4 constitutes a key component of microtubule-dependent mRNA transport in filaments of Ustilago maydis. Although a number of potential target mRNAs could be identified, cellular processes that depend on Rrm4-mediated transport remain largely unknown. Here, we used differential proteomics to show that ribosomal, mitochondrial, and cell wall-remodeling proteins, including the bacterial-type endochitinase Cts1, are differentially regulated in rrm4Δ filaments. In vivo UV crosslinking and immunoprecipitation and fluorescence in situ hybridization revealed that cts1 mRNA represents a direct target of Rrm4. Filaments of cts1Δ mutants aggregate in liquid culture suggesting an altered cell surface. In wild type cells Cts1 localizes predominantly at the growth cone, whereas it accumulates at both poles in rrm4Δ filaments. The endochitinase is secreted and associates most likely with the cell wall of filaments. Secretion is drastically impaired in filaments lacking Rrm4 or conventional kinesin Kin1 as well as in filaments with disrupted microtubules. Thus, Rrm4-mediated mRNA transport appears to be essential for efficient export of active Cts1, uncovering a novel molecular link between mRNA transport and the mechanism of secretion.
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Affiliation(s)
- Janine Koepke
- Heinrich-Heine University Düsseldorf, Institute for Microbiology, Düsseldorf, Germany
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Wang Y, Stary JM, Wilhelm JE, Newmark PA. A functional genomic screen in planarians identifies novel regulators of germ cell development. Genes Dev 2010; 24:2081-92. [PMID: 20844018 DOI: 10.1101/gad.1951010] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Germ cells serve as intriguing examples of differentiated cells that retain the capacity to generate all cell types of an organism. Here we used functional genomic approaches in planarians to identify genes required for proper germ cell development. We conducted microarray analyses and in situ hybridization to discover and validate germ cell-enriched transcripts, and then used RNAi to screen for genes required for discrete stages of germ cell development. The majority of genes we identified encode conserved RNA-binding proteins, several of which have not been implicated previously in germ cell development. We also show that a germ cell-specific subunit of the conserved transcription factor CCAAT-binding protein/nuclear factor-Y is required for maintaining spermatogonial stem cells. Our results demonstrate that conserved transcriptional and post-transcriptional mechanisms regulate germ cell development in planarians. These findings suggest that studies of planarians will inform our understanding of germ cell biology in higher organisms.
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Affiliation(s)
- Yuying Wang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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26
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Kraut-Cohen J, Gerst JE. Addressing mRNAs to the ER: cis sequences act up! Trends Biochem Sci 2010; 35:459-69. [DOI: 10.1016/j.tibs.2010.02.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 02/15/2010] [Accepted: 02/18/2010] [Indexed: 12/26/2022]
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Temme C, Zhang L, Kremmer E, Ihling C, Chartier A, Sinz A, Simonelig M, Wahle E. Subunits of the Drosophila CCR4-NOT complex and their roles in mRNA deadenylation. RNA (NEW YORK, N.Y.) 2010; 16:1356-1370. [PMID: 20504953 PMCID: PMC2885685 DOI: 10.1261/rna.2145110] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 04/16/2010] [Indexed: 05/27/2023]
Abstract
The CCR4-NOT complex is the main enzyme catalyzing the deadenylation of mRNA. We have investigated the composition of this complex in Drosophila melanogaster by immunoprecipitation with a monoclonal antibody directed against NOT1. The CCR4, CAF1 (=POP2), NOT1, NOT2, NOT3, and CAF40 subunits were associated in a stable complex, but NOT4 was not. Factors known to be involved in mRNA regulation were prominent among the other proteins coprecipitated with the CCR4-NOT complex, as analyzed by mass spectrometry. The complex was localized mostly in the cytoplasm but did not appear to be a major component of P bodies. Of the known CCR4 paralogs, Nocturnin was found associated with the subunits of the CCR4-NOT complex, whereas Angel and 3635 were not. RNAi experiments in Schneider cells showed that CAF1, NOT1, NOT2, and NOT3 are required for bulk poly(A) shortening and hsp70 mRNA deadenylation, but knock-down of CCR4, CAF40, and NOT4 did not affect these processes. Overexpression of catalytically dead CAF1 had a dominant-negative effect on mRNA decay. In contrast, overexpression of inactive CCR4 had no effect. We conclude that CAF1 is the major catalytically important subunit of the CCR4-NOT complex in Drosophila Schneider cells. Nocturnin may also be involved in mRNA deadenylation, whereas there is no evidence for a similar role of Angel and 3635.
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Affiliation(s)
- Claudia Temme
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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28
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Ryan S, Verghese S, Cianciola NL, Cotton CU, Carlin CR. Autosomal recessive polycystic kidney disease epithelial cell model reveals multiple basolateral epidermal growth factor receptor sorting pathways. Mol Biol Cell 2010; 21:2732-45. [PMID: 20519437 PMCID: PMC2912358 DOI: 10.1091/mbc.e09-12-1059] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have discovered that multiple basolateral pathways mediate EGF receptor sorting in renal epithelial cells. The polycystic kidney disease allele in the BPK mouse model, Bicc1, interferes with one specific EGF receptor pathway, causing nonpolar delivery of the receptor without affecting overall cell polarity. Sorting and maintenance of the EGF receptor on the basolateral surface of renal epithelial cells is perturbed in polycystic kidney disease and apical expression of receptors contributes to severity of disease. The goal of these studies was to understand the molecular basis for EGF receptor missorting using a well-established mouse model for the autosomal recessive form of the disease. We have discovered that multiple basolateral pathways mediate EGF receptor sorting in renal epithelial cells. The polycystic kidney disease allele in this model, Bicc1, interferes with one specific EGF receptor pathway without affecting overall cell polarity. Furthermore one of the pathways is regulated by a latent basolateral sorting signal that restores EGF receptor polarity in cystic renal epithelial cells via passage through a Rab11-positive subapical compartment. These studies give new insights to possible therapies to reconstitute EGF receptor polarity and function in order to curb disease progression. They also indicate for the first time that the Bicc1 gene that is defective in the mouse model used in these studies regulates cargo-specific protein sorting mediated by the epithelial cell specific clathrin adaptor AP-1B.
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Affiliation(s)
- Sean Ryan
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4970, USA
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29
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Fu Y, Kim I, Lian P, Li A, Zhou L, Li C, Liang D, Coffey RJ, Ma J, Zhao P, Zhan Q, Wu G. Loss of Bicc1 impairs tubulomorphogenesis of cultured IMCD cells by disrupting E-cadherin-based cell-cell adhesion. Eur J Cell Biol 2010; 89:428-36. [PMID: 20219263 PMCID: PMC2886128 DOI: 10.1016/j.ejcb.2010.01.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 01/20/2010] [Accepted: 01/28/2010] [Indexed: 01/12/2023] Open
Abstract
The Bicaudal-C (Bic-C) gene was originally discovered in Drosophila melanogaster. The gene product Bic-C is thought to serve as an RNA-binding molecule targeting diverse proteins at the post-transcriptional level. Recent research has shown this gene to be conserved in many species, from Caenorhabditis elegans to humans. Disruption of this protein can disturb the normal migration direction of the anterior follicle cell of Drosophila oocytes, while mutation of a mouse Bicc1 (a mouse homologue of Bic-C) results in phenotypes mimicking human hereditary polycystic kidney disease (PKD). However, the cellular function of Bicc1 gene products in mammalian systems remains largely unknown. In this study, we established stable IMCD (mouse inner medullary collecting duct) cell lines, in which Bicc1 was silenced by short hairpin RNA inhibition (shRNA). We show that inhibition of Bicc1 disrupted normal tubulomorphogenesis and induced cystogenesis of IMCD cells grown in three dimensional cultures. To determine what factors contributed to the defect, we systematically examined biological changes of Bicc1-silenced IMCD cells. We found that the cells had significant defects in E-cadherin-based cell-cell adhesion, along with abnormalities in actin cytoskeleton organization, cell-extracellular matrix interactions, cell proliferation, and apoptosis. These findings suggest that lack of Bicc1 leads to disruption of normal cell-cell junctions, which in turn impedes establishment of epithelial polarity. These cellular defects may initiate abnormal tubulomorphogenesis and cystogenesis of IMCD cells grown in vitro. The observation of aberrant cellular behaviors in Bicc1-silenced IMCD cells reveal functions for Bicc1 in renal epithelial cells and provides insight into a potential pathogenic mechanism of polycystic kidney disease.
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Affiliation(s)
- Yulong Fu
- Division of Translational Cancer Research and Therapy, State Key Laboratory of Molecular Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences, Beijing 100021, China
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Bouvrette DJ, Sittaramane V, Heidel JR, Chandrasekhar A, Bryda EC. Knockdown of bicaudal C in zebrafish (Danio rerio) causes cystic kidneys: a nonmammalian model of polycystic kidney disease. Comp Med 2010; 60:96-106. [PMID: 20412683 PMCID: PMC2855035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 12/05/2009] [Accepted: 12/09/2009] [Indexed: 05/29/2023]
Abstract
Polycystic kidney disease (PKD) is one of the leading causes of end-stage renal disease in humans and is characterized by progressive cyst formation, renal enlargement, and abnormal tubular development. Currently, there is no cure for PKD. Although a number of PKD genes have been identified, their precise role in cystogenesis remains unclear. In the jcpk mouse model of PKD, mutations in the bicaudal C gene (Bicc1) are responsible for the cystic phenotype; however, the function of Bicc1 is unknown. In this study, we establish an alternative, nonmammalian zebrafish model to study the role of Bicc1 in PKD pathogenesis. Antisense morpholinos were used to evaluate loss of Bicc1 function in zebrafish. The resulting morphants were examined histologically for kidney cysts and structural abnormalities. Immunostaining and fluorescent dye injection were used to evaluate pronephric cilia and kidney morphogenesis. Knockdown of zebrafish Bicc1 expression resulted in the formation of kidney cysts; however, defects in kidney structure or pronephric cilia were not observed. Importantly, expression of mouse Bicc1 rescues the cystic phenotype of the morphants. These results demonstrate that the function of Bicc1 in the kidney is evolutionarily conserved, thus supporting the use of zebrafish as an alternative in vivo model to study the role of mammalian Bicc1 in renal cyst formation.
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Affiliation(s)
- Denise J Bouvrette
- Genetics Area Program and Department of Veterinary Pathobiology, Research Animal Diagnostic Laboratory, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon
| | - Vinoth Sittaramane
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri
| | - Jerry R Heidel
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon
| | - Anand Chandrasekhar
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri
| | - Elizabeth C Bryda
- Genetics Area Program and Department of Veterinary Pathobiology, Research Animal Diagnostic Laboratory, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon
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Regulation of Drosophila vasa in vivo through paralogous cullin-RING E3 ligase specificity receptors. Mol Cell Biol 2010; 30:1769-82. [PMID: 20123973 DOI: 10.1128/mcb.01100-09] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Drosophila species, molecular asymmetries guiding embryonic development are established maternally. Vasa, a DEAD-box RNA helicase, accumulates in the posterior pole plasm, where it is required for embryonic germ cell specification. Maintenance of Vasa at the posterior pole requires the deubiquitinating enzyme Fat facets, which protects Vasa from degradation. Here, we found that Gustavus (Gus) and Fsn, two ubiquitin Cullin-RING E3 ligase specificity receptors, bind to the same motif on Vasa through their paralogous B30.2/SPRY domains. Both Gus and Fsn accumulate in the pole plasm in a Vasa-dependent manner. Posterior Vasa accumulation is precocious in Fsn mutant oocytes; Fsn overexpression reduces ovarian Vasa levels, and embryos from Fsn-overexpressing females form fewer primordial germ cells (PGCs); thus, Fsn destabilizes Vasa. In contrast, endogenous Gus may promote Vasa activity in the pole plasm, as gus females produce embryos with fewer PGCs, and posterior accumulation of Vas is delayed in gus mutant oocytes that also lack one copy of cullin-5. We propose that Fsn- and Gus-containing E3 ligase complexes contribute to establishing a fine-tuned steady state of Vasa ubiquitination that influences the kinetics of posterior Vasa deployment.
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Maisonneuve C, Guilleret I, Vick P, Weber T, Andre P, Beyer T, Blum M, Constam DB. Bicaudal C, a novel regulator of Dvl signaling abutting RNA-processing bodies, controls cilia orientation and leftward flow. Development 2009; 136:3019-30. [PMID: 19666828 DOI: 10.1242/dev.038174] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Polycystic diseases and left-right (LR) axis malformations are frequently linked to cilia defects. Renal cysts also arise in mice and frogs lacking Bicaudal C (BicC), a conserved RNA-binding protein containing K-homology (KH) domains and a sterile alpha motif (SAM). However, a role for BicC in cilia function has not been demonstrated. Here, we report that targeted inactivation of BicC randomizes left-right (LR) asymmetry by disrupting the planar alignment of motile cilia required for cilia-driven fluid flow. Furthermore, depending on its SAM domain, BicC can uncouple Dvl2 signaling from the canonical Wnt pathway, which has been implicated in antagonizing planar cell polarity (PCP). The SAM domain concentrates BicC in cytoplasmic structures harboring RNA-processing bodies (P-bodies) and Dvl2. These results suggest a model whereby BicC links the orientation of cilia with PCP, possibly by regulating RNA silencing in P-bodies.
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Stagner EE, Bouvrette DJ, Cheng J, Bryda EC. The polycystic kidney disease-related proteins Bicc1 and SamCystin interact. Biochem Biophys Res Commun 2009; 383:16-21. [PMID: 19324013 DOI: 10.1016/j.bbrc.2009.03.113] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 03/19/2009] [Indexed: 12/27/2022]
Abstract
Mutations in either the Bicaudal-C or the Anks6 gene which encode the Bicc1 and SamCystin proteins respectively cause formation of renal cysts in rodent models of polycystic kidney disease, however their role in the mammalian kidney is unknown. Immunolocalization studies demonstrated that, unlike many other PKD-related proteins, SamCystin and Bicc1 do not localize to the primary cilia of cultured kidney cells. Epitope-tagged recombinant SamCystin and Bicc1 proteins were transiently transfected into inner medullary collecting duct (IMCD) cells and co-immunoprecipitated. The results showed that SamCystin self-associates, Bicc1 and SamCystin interact, the mutation responsible for PKD in the Han:SPRD-Cy rat disrupts the self-association of SamCystin but not the Bicc1-SamCystin interaction, and RNA may be an important component of the Bicc1-SamCystin complex. These studies provide the first evidence that Bicc1 and SamCystin interact at the protein level suggesting that they function in a common molecular pathway that when perturbed, is involved in cystogenesis.
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Affiliation(s)
- Emily E Stagner
- Department of Veterinary Pathobiology, University of Missouri, Columbia, 65211, USA
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