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Composition and dynamics of BicD and Cbp transport particles

English title Composition and dynamics of BicD and Cbp transport particles
Applicant Suter Beat
Number 135436
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 01.07.2011 - 30.06.2014
Approved amount 537'000.00
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All Disciplines (5)

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

Keywords (6)

Drosophila; mRNA localization; Cbp; Oogenesis; Bic-D RNPs; Microtubule transport

Lay Summary (English)

Lead
Lay summary

Cells need to become polarized to develop and function properly.For this purpose cellular transport systems move different cargo complexescontaining mRNAs, proteins and organelles to their final destination. Thesetransport processes arose early during evolution and, because of theirimportance, they remained conserved from simple model organisms up to humans.This allows us to study them in systems that can easily be manipulated withmolecular genetics tools, knowing that the results we find will also tell ushow these mechanisms work in human beings.

As astart to understand these transport processes we have analyzed the proteincomposition of such localizing complexes. As a related next step we now want tofind out which mRNAs use this transport system. For this we will isolate thecomplexes, extract the mRNA from them and identify them by sequencing. It willthen be interesting to correlate the biochemically identified mRNAs with thesubcellular localization patterns of these mRNAs because it is possible thatonly mRNAs with a distinct localization pattern are present in these complexes.This would therefore give a good hint about the function of these localizationcomplexes.

. Oursecond objective is to figure out the role of one of the novel mRNA bindingproteins in the localization complexThis protein, Cbp80,is usually found in the nucleus where some of its functions are know. However,in our case it is present in these special complexes in the cytoplasm and thisleaves room for attractive speculations about what it is doing there. These hypothesesneed to be tested now.

Ourthird objective is based on the knowledge that the transport complexes weidentified are dynamic. They change over time and multiple different complexesexist at any time point. We are fascinated by this dynamics and believe thatunderstanding this dynamics is key to the understanding of how one transportsystem is capable of localizing different cargos

 

Forinstance we believe that we will be able to find out whether individual cargois tagged to be delivered directly to its final destination or whether relatedcargo are transported together to a sorting station, where they aredisassembled and resorted for their next destination.

DrosophilaWith this proposed work we can be confident that we will be ableto continue to establish novel concepts in the cell biology of development. Theissues we address here are very general because already during embryonicdevelopment of more than 71% of the mRNAs show asubcellular localization pattern. Furthermore, mRNA localization is aparticularly interesting concept because it efficiently focuses expression ofproteins to specific regions of a cell. 

Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Clathrin heavy chain plays multiple roles in polarizing the Drosophila oocyte downstream of Bic-D
Vazquez-Pianzola Paula (2014), Clathrin heavy chain plays multiple roles in polarizing the Drosophila oocyte downstream of Bic-D, in Development, 141, 1915.
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, ID 274196.
Lissencephaly-1 promotes the recruitment of dynein and dynactin to transported mRNAs
Dix Carly I., Soundararajan Harish Chandra, Dzhindzhev Nikola S., Begum Farida, Suter Beat, Ohkura Hiroyuki, Stephens Elaine, Bullock Simon L. (2013), Lissencephaly-1 promotes the recruitment of dynein and dynactin to transported mRNAs, in J. Cell Biol., 202(3), 479-494.
Conservation of the RNA Transport Machineries and Their Coupling to Translation Control across Eukaryotes.
Vazquez-Pianzola Paula, Suter Beat (2012), Conservation of the RNA Transport Machineries and Their Coupling to Translation Control across Eukaryotes., in Comparative and functional genomics, 2012, 287852-287852.
Drosophila sosie functions with bH-Spectrin and actin organizers in cell migration, epithelial morphogenesis and cortical stability
Urwyler Olivier, Cortinas-Elizondo Fabiola, Suter Beat (2012), Drosophila sosie functions with bH-Spectrin and actin organizers in cell migration, epithelial morphogenesis and cortical stability, in Biology Open, 1(994–1005), 994-1005.
Pabp binds to the osk 3'UTR and specifically contributes to osk mRNA stability and oocyte accumulation.
Vazquez-Pianzola Paula, Urlaub Henning, Suter Beat (2011), Pabp binds to the osk 3'UTR and specifically contributes to osk mRNA stability and oocyte accumulation., in Developmental biology, 357(2), 404-18.

Collaboration

Group / person Country
Types of collaboration
University of Cologne Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
MRC Laboratory of Molecular Biology Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Max Planck Institute for Biophysical Chemistry 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
Gene Translation: Fidelity and Quality Control Poster Determinants of PheRS accuracy in translation and their role in development and physiology of a higher eukaryote. 02.12.2013 Barcelona, Spain Suter Beat;
RNA 2013 Talk given at a conference Novel players and novel mRNAs transported by the Bic-D / Egl / Dynein RNA localization machinery 11.06.2013 Davos, Switzerland Rashpa Ravish; Vazquez Paula; Suter Beat;
Riboclub meeting Poster A role for Bic-D in the endocytic pathway by localizing Chc mRNA into the oocyte 24.09.2012 Sherbrooke, Canada, Canada Suter Beat; Vazquez Paula;


Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Wiso unsere Körper überhaupt altern Berner Zeitung German-speaking Switzerland 2012

Awards

Title Year
EMBO postdoctoral fellowship: DEAD box RNA helicases regulate the activity of Casein kinase 1 2013

Associated projects

Number Title Start Funding scheme
153280 Composition of different BicD/ mRNA complexes and function of cytoplasmic Cbp80 01.07.2014 Project funding
145013 Multimode Live Imaging - University of Bern (MLI-be) 01.04.2013 R'EQUIP
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
150824 White-Laser Confocal Microscopy: Modular and Sensitive Multi-channel Analysis 01.12.2013 R'EQUIP
120635 Molecular and Genetic Dissection of the BicD Localization Machinery 01.07.2008 Project funding

Abstract

Many eukaryotic cells become polarized to develop and function properly. Such cellular asymmetries are often created by the microtubule cytoskeleton and by transport of specific RNAs, proteins and organelles on these tracks. mRNA localization is a particularly interesting concept because it efficiently focuses expression of proteins to specific regions of a cell. A small number of plus-end directed microtubule motors (kinesins) and even fewer minus-end directed motors (cytoplasmic dynein) transport different types of cargos to their appropriate cellular compartments. This is possible because adaptor molecules couple different types of cargo to the motors. The BicD family proteins function as such linkers that couple the cytoplasmic dynein motor with cargo as diverse as different RNPs, vesicles and even large organelles.During embryonic development of Drosophila more than 71% of the mRNAs show a subcellular localization pattern, underscoring the importance of the localization mechanism. It is expected that many of the localized mRNAs use the Bic-D/Egl transport machinery or a similar transport system for their localization. We hypothesize that by studying the composition and dynamics of the different BicD particles with their amazing variety of cargo, we can identify the most important principles of the mechanism of function of this highly complex system. Our specific objectives for this granting period will be the following ones.Objective 1) Identification of mRNAs associated with and transported by BicD.Through independent immunopurifications, BicD- and Egl- associated mRNAs will be purified, reverse transcribed and identified using high-throughput sequencing (deep sequencing). In this way we will attempt to get a quantitative and comprehensive picture of the mRNAs in these RNPs. These mRNAs will then be further sub-grouped according to their localization pattern, their requirement for BicD for their localization, and their cellular functions (if known). The grouped sequence data may also allow the identification of BicD-RNP- or terminal localization elements.Objective 2: Identifying the function of Cbps in the BicD localization processes.Cbp80, the larger of the subunits of the Cbp80/Cbp20 “nuclear” cap binding complex Cbc, physically interacts with BicD. Cbc has described roles in splicing, nuclear export, mRNA stability and NMD (non-sense mediated decay of mRNAs) and (the pioneer round of) translation of mRNAs), but it also seems to be able to function in the cytoplasm. We will analyze the molecular interactions between Cbc and BicD and find out where in the cell the two proteins can be found in the same particles. A functional analysis of Cbc will be initiated at the genetic level and complemented by a biochemical / molecular approach, designed to find out which mRNAs are associated with Cbp80 in the cytoplasm. In the long run, we will then choose a select set of Cbc targets for a detailed analysis of the role of Cbc in the localization process as well as for the function of these targets.Objective 3) Revealing composition and dynamics of different BicD transport particles. Because of the variety of the different types of cargos that BicD hooks up for transport, we want to know whether individual particles are homogenous for the type of cargo they contain. One BicD particle may for instance only contain one specific mRNA type or it may contain different mRNAs that end up in the same location. Alternatively, a transport particle may contain different mRNAs and, in addition, also vesicle cargo. We will study the distribution of different mRNAs from one localization class, then from classes that show a different localization pattern. For this purpose we will use a quantitative RNA in situ hybridization protocol. Live imaging of selected pairs of localizing mRNAs will then be used to find out whether and where mRNP particles get resorted during the transport. As extension of the RNP work, we will subsequently also establish the relationship between RNP and vesicle containing cargo particles through a combination of IP and immunolocalization experiments with the additional adaptor proteins involved in the different processes. With this proposed work we can be confident that we will be able to continue to establish novel concepts that will be further tested and developed in different systems and that will again be relevant for all metazoans, including humans.
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