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Composition of different BicD/ mRNA complexes and function of cytoplasmic Cbp80

English title Composition of different BicD/ mRNA complexes and function of cytoplasmic Cbp80
Applicant Suter Beat
Number 153280
Funding scheme Project funding
Research institution Institut für Zellbiologie Departement Biologie Universität Bern
Institution of higher education University of Berne - BE
Main discipline Embryology, Developmental Biology
Start/End 01.07.2014 - 31.10.2017
Approved amount 525'000.00
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All Disciplines (5)

Discipline
Embryology, Developmental Biology
Genetics
Molecular Biology
Biochemistry
Cellular Biology, Cytology

Keywords (6)

Microtubule transport; Cbp; RNPs; mRNA localization; Drosophila; BicD, Bic-D

Lay Summary (German)

Lead
Der Transport von mRNAs in spezifische zelluläre Kompartimente dient der räumlichen (und zeitlichen) Kontrolle der Aktivität von Genen und ihren Produkten. Wir studieren im Drosophila Modellsystem die Komponenten, welche am Transport und der Translationskontrolle von mRNAs beteiligt sind und wir studieren die mRNAs, die auf diese Weise reguliert werden.
Lay summary

Genetisch Information muss zeitlich und räumlich kontrolliert umgesetzt werden. Wir haben ein zelluläres Transportsystem entdeckt, dass die mRNA, die Information der Gene, an die korrekte Stelle in der Zelle bringt, wo diese zum richtigen Zeitpunkt aktiviert wird und ihre Funktion kontrolliert erfüllen kann. Eine neu entdeckte Komponente von diesem Transportsystem hat auch weitere Funktionen bei der Synthese der mRNA und bei der Verteidigung des Erbgutes gegen parasitierende Elemente. Wir wollen die Funktionen dieses neuen Elementes nun im Detail studieren.

Dieses mRNA Transportsystem kommt in unterschiedlicher Zusammensetzung vor und übt je nachdem verschiede Funktionen aus. Wir haben schon einige der transportierten mRNAs identifiziert und wollen nun herausfinden, welche Komplexe mit welchen mRNAs assoziieren und was deren Funktionen sind. In mehreren Fällen konnten wir die Lokalisation schon mit einer lokalen Funktion korrelieren. Es scheint also, als würden die mRNAs wirklich von unserem Transportsystem an den Ort gebracht, wo sie dann zum gegebenen Zeitpunkt aktiv sein müssen. Wir wollen dies nun an speziellen Beispielen noch klar demonstrieren.

Es ist technisch sehr schwierig diese Transportvorgänge direkt in der lebenden Zelle zu zeigen. Die meisten Daten beruhen daher auf Experimenten, die interpretiert werden müssen und wir schliessen dann aus den Resultaten indirekt, dass diese Vorgänge so ablaufen. Da die technischen Hilfsmittel immer besser werden, wird es uns vielleicht aber doch bald möglich, diese Vorgänge im lebenden Tier oder Organ sichtbar zu machen, zu filmen und damit direkt zu zeigen.

Hierbei handelt es sich um Grundlagenforschung, die auch für die medizinische Forschung relevant ist. Die Arbeiten werden im Drosophila Modellsystem ausgeführt.

 

Direct link to Lay Summary Last update: 03.06.2014

Responsible applicant and co-applicants

Employees

Publications

Publication
Cbp80 is needed for the expression of piRNA components and piRNAs
Rashpa Ravish, Vazquez-Pianzola Paula, Colombo Martino, Hernandez Greco, Beuchle Dirk, Berger Fabienne, Peischl Stephan, Bruggmann Rémy, Suter Beat (2017), Cbp80 is needed for the expression of piRNA components and piRNAs, in PLOS ONE, 12(7), e0181743-e0181743.
The mRNA transportome of the BicD/Egl transport machinery
Vazquez-Pianzola Paula, Schaller Bogdan, Colombo Martino, Beuchle Dirk, Neuenschwander Samuel, Marcil Anne, Bruggmann Rémy, Suter Beat (2016), The mRNA transportome of the BicD/Egl transport machinery, in RNA Biology, 14(1), 73-89.
translin Is Required for Metabolic Regulation of Sleep
Murakami Kazuma, Yurgel Maria E., Stahl Bethany A., Masek Pavel, Mehta Aradhana, Heidker Rebecca, Bollinger Wesley, Gingras Robert M., Kim Young-Joon, Ja William W., Suter Beat, DiAngelo Justin R., Keene Alex C. (2016), translin Is Required for Metabolic Regulation of Sleep, in Current Biology, 26(7), 972-980.
A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis
Börner Kenneth, Jain Dhawal, Vazquez-Pianzola Paula, Vengadasalam Sandra, Steffen Natascha, Fyodorov Dmitry V., Tomancak Pavel, Konev Alexander, Suter Beat, Becker Peter B. (2016), A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis, in Developmental Biology, 411(2), 217-230.
The aminoacyl-tRNA synthetases of Drosophila melanogaster
Lu Jiongming, Marygold Steven J, Gharib Walid H, Suter Beat (2016), The aminoacyl-tRNA synthetases of Drosophila melanogaster, in Fly, 9(2), 53-61.
Evolution of the Molecules Coupling mRNA Transport with Translational Control in Metazoans.
Vazquez-Pianzola Paula, SuterBeat, Hernández Grecco (2016), Evolution of the Molecules Coupling mRNA Transport with Translational Control in Metazoans., in Hernández G. & Jagus R. (ed.), Cham: Springer International Publishing, Switzerland, 531-546.
A Drosophila XPD model links cell cycle coordination with neuro-development and suggests links to cancer
Stettler K., Li X., Sandrock B., Braga-Lagache S., Heller M., Dumbgen L., Suter B. (2015), A Drosophila XPD model links cell cycle coordination with neuro-development and suggests links to cancer, in Disease Models & Mechanisms, 8(1), 81-91.
Double-sieving-defective aminoacyl-tRNA synthetase causes protein mistranslation and affects cellular physiology and development
Lu Jiongming, Bergert Martin, Walther Anita, Suter Beat (2014), Double-sieving-defective aminoacyl-tRNA synthetase causes protein mistranslation and affects cellular physiology and development, in Nature Communications, 5, 5650-5650.
Clathrin heavy chain plays multiple roles in polarizing the Drosophila oocyte downstream of Bic-D
Vazquez-Pianzola Paula, Adam Jacqueline, Haldemann Dominique, Hain Daniel, Urlaub Henning, Suter Beat (2014), Clathrin heavy chain plays multiple roles in polarizing the Drosophila oocyte downstream of Bic-D, in Development, 141(9), 1915-1926.
Cross Talk between Cellular Regulatory Networks Mediated by Shared Proteins
Dolde Christine, Lu Jiongming, Suter Beat (2014), Cross Talk between Cellular Regulatory Networks Mediated by Shared Proteins, in Advances in Biology, 2014, 1-12.
A CK1 FRET biosensor reveals that DDX3X is an essential activator of CK1ε
Dolde Christine, Grüter Simon, Bischof Joachim, Montada Anna, Halekotte Jakob, Peifer Christian, Kalbacher Hubert, Baumann Ulrich, Knippschild Uwe, Suter Beat, A CK1 FRET biosensor reveals that DDX3X is an essential activator of CK1ε, in J Cell Science, 131(1), 1-13.

Collaboration

Group / person Country
Types of collaboration
Hubert Kalbacher/University of Tübingen Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Simon Bullock / MRC Cambridge Great Britain and Northern Ireland (Europe)
- Publication
Ulrich Baumann/University of Cologne Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Steven J Marygold/Flybase Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Christian Peifer/Christian Albrechts University Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Greco Hernandez/National Institute for Cancer Mexico (North America)
- in-depth/constructive exchanges on approaches, methods or results
Uwe Knippschild/Ulm University Hospital Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Alex C. Keene/University of Nevada & Florida Atlantic University United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Rémy Bruggmann/University of Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Björn Sandrock/Philipps-University Marburg Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Manfred Heller / Universität Bern Switzerland (Europe)
- Publication
- Research Infrastructure
Jakob Halekotte/Christian Albrechts University Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Fisher / Mount-Sinai Med School United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Exchange of personnel
Hening Urlaub / Max Planck Institute Göttingen Germany (Europe)
- Publication
Peter Becker/Ludwig-Maximilians-University, Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
11th Aminoacyl-tRNA Synthetases Symposium (AARS2017) Poster Noncanonical function of Phenylalanyl tRNA synthetase 29.10.2017 Florida, United States of America Brunssen Dominique; Suter Beat; Ho Manh Tin;
European Drosophila Research Conference (EDRC) 2017 Poster Investigating the cell cycle regulatory mechanism of Mms19 in Drosophila melanogaster. 22.09.2017 London, Great Britain and Northern Ireland Nag Rishita; Chippalkatti Rohan; Suter Beat;
Swiss Fly meeting 2017 Poster nvestigating the cell cycle regulatory mechanism of Mms19 in Drosophila melanogaster. 09.06.2017 Bern, Switzerland Nag Rishita; Chippalkatti Rohan; Suter Beat;
7th Annual BeFri Research Retreat 2017 Poster Noncanonical function of Phenylalanyl tRNA synthetase 06.05.2017 Kandersteg, Switzerland Brunssen Dominique; Suter Beat; Ho Manh Tin;
GCB Symposium 2017 Poster Noncanonical function of Phenylalanyl tRNA synthetase 02.02.2017 Bern, Switzerland Ho Manh Tin; Brunssen Dominique;
From structural Biology to Drug Discovery (Summer school) Talk given at a conference The many lifes for PheRS, known mainly as aminoacyl tRNA synthetse 01.09.2016 Anavyssos, Greece Suter Beat;
Swiss Fly meeting 2016 Poster Investigating the cell cycle regulatory mechanism of Mms19 in Drosophila melanogaster. 10.06.2016 Zürich, Switzerland Chippalkatti Rohan; Suter Beat; Nag Rishita;
Swiss Drosophila Meeting 2016 Poster Phenylalanyl tRNA synthetase: non canonical functions in development 10.06.2016 Zürich, Switzerland Suter Beat; Brunssen Dominique; Ho Manh Tin;
Swiss Meeting on Genome Stability and Chromatin Dynamics Talk given at a conference Mms19 is a mitotic gene required for proper Cdk activity and chromosome segregation 09.06.2016 Emmetten, Switzerland Suter Beat;
BeFri Research Retreat Poster Investigating the cell cycle regulatory mechanism of Mms19 in Drosophila melanogaster. 04.05.2016 Kandersteg, Switzerland Chippalkatti Rohan; Suter Beat; Nag Rishita;
6th Annual BeFri Research Retreat 2016 Poster Phenylalanyl tRNA synthetase: non canonical functions in development 28.04.2016 Kandersteg, Switzerland Brunssen Dominique; Ho Manh Tin; Suter Beat;
Spring meeting of the graduate school of Molecular Medicine Talk given at a conference A novel cell cycle function of XPD prevents chromosomal instability and mitotic defects in an animal model 06.04.2016 Ulm, Germany Suter Beat;
aaRS meeting Barcelona Talk given at a conference Growth tuning by Drosophila PheRS 18.10.2015 Barcelona, Spain Suter Beat;
Seminar Individual talk Safeguards for decoding the genetic codes: roles of molecular sieves that ensure specificity of tRNAPhe aminoacylation 15.10.2015 Barcelona, Spain Suter Beat;
EDRC Poster Mms19 is a mitotic gene 09.09.2015 Heidelberg, Germany Nag Rishita;
Swiss Drosophila workshop annual meeting 2015 & 2016 Poster generally 2 posters per meeting 24.04.2015 Fribourg, Zürich, Switzerland Chippalkatti Rohan; Grubesic Slobodan; Ho Manh Tin; Brunssen Dominique; Suter Beat; Dolde Christine; Grüter Simon; Nag Rishita;
Swiss Drosophila workshop annual meeting 2015 & 2016 Talk given at a conference Generally 1 talk per meeting 24.04.2015 Fribourg, Zürich, Switzerland Nag Rishita;
Seminar Individual talk Safeguards for decoding the genetic codes: roles of molecular sieves that ensure specificity of tRNAPhe aminoacylation 29.10.2014 Köln, Germany Suter Beat;


Self-organised

Title Date Place
Swiss Drosophila Workshop, annual meeting 2017 09.06.2017 Bern, Switzerland

Associated projects

Number Title Start Funding scheme
177096 A high content confocal microscope for fast 3D imaging of living samples 01.10.2018 R'EQUIP
150824 White-Laser Confocal Microscopy: Modular and Sensitive Multi-channel Analysis 01.12.2013 R'EQUIP
135436 Composition and dynamics of BicD and Cbp transport particles 01.07.2011 Project funding
173188 Drosophila BicD family members: mitotic functions, structural aspects of RNA localization, and functional characterization of a novel member 01.11.2017 Project funding
120635 Molecular and Genetic Dissection of the BicD Localization Machinery 01.07.2008 Project funding
117446 Fast, accurate, and sensitive mass spectrometry for basic research in life sciences at the university of bern / mass spectrometer 01.10.2007 R'EQUIP

Abstract

A large proportion of the cellular mRNAs exhibit specific distribution patterns that relate to the local function of the proteins they encode. The BicD/ Egl transport machinery localizes many mRNAs to their target site by attaching the cargo to the negative-end directed microtubule motor dynein. Surprisingly, BicD and dynein also transport vesicles and large organelles. We have dissected this transport system using genetic and biochemical tools, allowing us to learn much about composition and dynamics of the different BicD complexes and about the function of some of the BicD-associated proteins. Recently we focused on the role of Cbp80 in oogenesis and found that it acts together with Piwi and P-body components in repressing mRNAs that are being localized. We also identified the transcriptome that associates with BicD/ Egl. During the upcoming granting period we will focus on the analysis of the BicD/ RNA binding protein complexes and on the novel functions of Cbp80.Objective 1: The cytoplasmic functions of Cbp80Cbp80 is known to function in the nucleus, but we uncovered its additional activities in the cytoplasm, where it represses mRNAs that are on the move to their target location. We therefore want to find out to what mRNAs Cbp80 is bound to in the cytoplasm of syncytial Drosophila embryos. For this purpose we will isolate cytoplasmic fractions, purify Cbp80-tag complexes and determine their RNA content with the RNA-IP-Seq (RIPSeq) protocol we established successfully for BicD/ Egl::GFP complexes. We will take advantage of the local Illumina high throughput sequencing facility and the Bernese Bioinformatics group. Using the top ranking mRNAs associated with cytoplasmic Cbp80 we will test whether they are normally translationally repressed, localized, degraded at a specific time point, or whether they display another specific feature. This should reveal the functions of cytoplasmic Cbp80 that we will then test experimentally.Objective 2: Role of Cbp80 in the piRNA pathway We found that Cbp80 interacts with Piwi and it seems to function to localize it into the nucleus, which is essential to start the primary piRNA biogenesis cycle that causes transcriptional silencing of transposable elements (TEs). A role of Cbp80 in the piRNA pathway had so far not been described. To assess transcritptional silencing of TEs we will therefore compare the chromatin structure of the germ line nuclei in the “TE grave yard” regions with and without knock down of Cbp80. Objective 3: Correlating complexes with mRNA targets and RBPs BicD interacts with many different RNA-binding proteins (RBPs) and with some of them in a mutually exclusive manner. We have identified the Egl targets, and will next identify the targets of the other RBPs. We then want to compare the different data sets to learn more about the different complexes. Aside from BicD, Egl and Cbp80 targets, these are mainly FMRP and IMP targets.Objective 4: Role of early apical localization and early embryonic gene expression controlThe Egl targets revealed interesting novel questions. Acf1 (ATP-dependent chromatin assembly factor 1) mRNA localizes to the apical cortex of young embryos. It encodes a nucleosome-remodeling factor involved in chromatin assembly and gene repression. Its protein expression is strictly controlled, localizing to the pericentric heterochromatin. Interestingly, the blastodermal heterochromatin assembles at the apical pole of the nuclei, where Acf1 protein accumulates and adjacent to the cytoplasm where its mRNA is localized! Furthermore, this heterochromatin formation needs Acf1, and FMRP is also involved in this process. We will test whether Acf1 mRNA localization is important for this localized heterochromatin formation.The second gene of interest is sry-a. The protein it encodes is apically localized and essential for cellularization. There are only 4 zygotic genes known to induce cellularization and it seems that their expression is tightly controlled to ensure it does happen only after 13 nuclear division cycles. This led to our hypothesis that we may be able to cause insect embryos to cellularize prematurely if we express these genes prematurely. We will test this hypothesis with simple experiments. Objective 5: live analysis of BicD-dependent transport, cytoplasmic streaming and sortingExperiments addressing the transport dynamics of native mRNAs expressed during oogenesis are technically challenging. We plan two different types of experiments, one to analyze pairwise the distribution of mRNAs that may be co-transported in one complex and one to analyze co-transport of two different protein / organelle cargos that show similar localization patterns.We also identified an earlier fast cytoplasmic streaming event that is involved in establishing the earliest polarities in the female germ line of Drosophila. Because this process seems to be very important for polarity formation we will study it in greater detail.
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