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INTERNATIONAL VOLUNTEER PROGRAM
APPLICATION FORM
Date of application: 23/12/2012
Person responsible for this proposal
Name:
Position:
Institution:
Address:
Phone:
E-mail:
Orna Amster-Choder
Professor
Hebrew University
The Hebrew University Faculty of Medicine, P.O.Box 12272, Jerusalem 91120, Israel
972-2-675-8460; 972-54-882-0440
[email protected]
Name of the laboratory and host institution
Host institution:
Department:
Laboratory:
Hebrew University
Microbiology and Molecular Genetics
Prof. Amster-Choder’s laboratory
Title of the research project in which the volunteer would be involved
Comprehensive mapping of RNA architecture in bacterial cells
Have you already identified a candidate?
NO 
The candidate should have a good background in molecular biology and speak good English.
Preferentially, he/she should have some background in microbiology, biochemistry and
microscopy.
Suitable date for
receiving the volunteer
Flexible
French Embassy in Israel
Office for Science & Technology
Rothschild Boulevard 7
Tel Aviv, 66881 Israel
Duration of the stay
Required participation
from the host institution
in the monthly allowance
24 months
Tel: +972 (0)3 796 80 42
Fax: +972 (0)3 796 80 45
Website: fitscience.wordpress.com
Email: [email protected]
750 EUR (3720 ILS)
Description of the specific research work, which would be carried out
Background: The scarcity of membrane-bounded organelles in bacteria led to the assumption that
proteins and RNA are distributed randomly throughout the cell. This view has changed
considerably and studies in the last decade revealed that bacterial cells localize proteins to
specific subcellular domains. However, due to the lack of nucleus and to the coupling between
transcription and translation, the general thinking in the field has been that localization of
bacterial proteins depends solely on targeting signals within the proteins. Therefore, the
localization of RNA transcripts in bacterial cells remained poorly characterized.
Our surprising discovery (Nevo-Dinur et al., 2011, Science, 331:1081-1084), which has been chosen
as one of the breakthroughs of the 2011 year (Adler, 2012, Sci Signal, 5:eg1, doi:
10.1126/scisignal.2002787), that bacterial mRNAs localize to subcellular domains where their
protein products are required, in a translation-independent manner, changed this dogma and
strengthen the view that clustering and compartmentalization are central themes that underlie
spatio-temporal control of molecular processes in all types of cells.
A high-throughput approach that we recently took corroborated the existence of significant
correlation between RNA localization and function in bacteria (unpublished data).
Based on our results, we hypothesize that the mechanistic basis for separating transcription and
translation is more primitive than assumed and did not co-evolve with the nucleus. The relative
simplicity of bacterial systems and the ease of their handling and genetic manipulation provides a
powerful tool to obtain a general picture of the mechanisms that link cell architecture and
function, which can then be extrapolated to improve our understanding of these mechanisms in
more complex organisms.
Goal: Our general goal is to explore the novel field of RNA localization in bacterial cells. More
specifically, the goal of the International volunteer’s project will be to obtain a subcellular RNA
contact map at high-resolution for different bacteria, as well as for mitochondria, which is of a
bacterial ancestry. The relative simplicity of bacterial pathways and machineries provides an
opportunity to obtain a general picture that can then be extrapolated to study more complex
organisms.
French Embassy in Israel
Office for Science & Technology
Rothschild Boulevard 7
Tel Aviv, 66881 Israel
Tel: +972 (0)3 796 80 42
Fax: +972 (0)3 796 80 45
Web : http://www.fitscience.wordpress.com
Email : [email protected]
Methodology: In the last decade, high-throughput techniques were developed to detect genomic
regions that are in spatial close proximity in vivo, i.e., Hi-C that uses high-throughput sequencing
to globally map chromatin contacts, allowing the derivation of high-resolution three-dimensional
contact maps of genomes (Lieberman-Aiden et al., 2009, Science 326:289-93). We wish to develop
an analogous methodology to derive contact maps of transcriptomes. More specifically, the idea is
to obtain RNA contact maps for whole bacterial cells and for minicells, which package only the
polar contact, as well as for mitochondria. Obtaining contact maps at different environmental
conditions will enable to discover key players in cell organization. Contact maps of strains deleted
for certain sRNAs will depict the extent of sRNA involvement in cell organization.
Significance: The suggested studies will advance our knowledge of mechanisms that link cell
architecture and function. We hope to reveal universal strategies for RNA localization that are
relevant to all types of cells, as well as bacterial-specific cues and mechanisms. Deciphering
universal mechanisms gains further importance in light of the growing list of diseases known to be
associated with defective RNA localization. Understanding features that are unique to bacteria is
important both for our understanding of the majority of the cells in our body, i.e., the microbiome,
and for the development of novel antibacterial drugs.
French Embassy in Israel
Office for Science & Technology
Rothschild Boulevard 7
Tel Aviv, 66881 Israel
Tel: +972 (0)3 796 80 42
Fax: +972 (0)3 796 80 45
Web : http://www.fitscience.wordpress.com
Email : [email protected]