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Sequencing of the bacillus subtilis genome

Objective

The objective is to determine, before the end of 1997, the entire genome sequence of Bacillus subtilis which is both of industrial importance and a model organism for Gram-positive bacteria. An international agreement has been reached allowing the allocation of regions of the chromosome among the groups of the European and Japanese Bacillus subtilis genome sequencing networks. This international project currently includes 17 European and 7 Japanese laboratories, together with 2 biotechnology companies (Genencor International and Novo Nordisk) and 1 Korean laboratory.
The European sequencing groups have obtained support from the European Commission (this contract and contract BIO2 CT-930272). The initial objective of this project (contract BIO2 CT-942011) was to determine the DNA sequence of about 10 % of the Bacillus subtilis genome (0.45 Mbp). To match this deadline, three high throughput sequencing groups have recently been integrated in this contract as subcontractors (see below).
A cloning strategy for the construction of gene banks representative of the entire B.acillus subtilis chromosome is not available. This is, at least in part, due to the generally high level of expression of Bacillus subtilis genes observed in Escherichia coli, leading to toxic effects in this commonly used cloning host. However, participating groups have employed a variety of strategies to overcome this limitation. They include: (1) cloning into a range of plasmid, lambda and YAC vectors; (2) the use of an Escherichia coli strain that lowers the copy number of ColE1-based plasmids and which correspondingly reduces the potential toxic effects of cloned genes; (3) the use of integrative plasmids and marker rescue in genome walking experiments; (4) in vitro amplification using standard, long-range (LR PCR) and inverse PCR techniques.
MAJOR SCIENTIFIC BREAKTHROUGHS AND INDUSTRIAL APPLICATIONS:
During this contract 0.74 Mbp of Bacillus subtilis DNA has been sequenced. The European sequencing network has presently deposited a total of 1.9 Mbp of new B. subtilis DNA sequence at the database maintained by the Institut Pasteur, confirming the leader position of the EU in the systematic sequencing of this genome. In the current EU framework, a relational database containing 3.6 Mbp of non redundant B. subtilis DNA sequences, representing 86 % of the total genome, has been constructed at the Institut Pasteur.
An industrial platform has been set up to facilitate contacts between project participants and European biotechnology companies. The following companies have agreed to this mode of cooperation: DuPont de Nemours (France), Genencor (Finland, USA), F. Hoffmann-La Roche AG (Switzerland), Novo Nordisk (Denmark), Puratos (Belgium), Roussel Uclaf (France), SmithKline Beecham Pharmaceuticals (United Kingdom). Moreover, a confidential document containing a list of similarities of B. subtilis proteins with known gene products is forwarded by the coordinator, at regular intervals, to the companies mentioned above.

Fields of science

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Call for proposal

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Funding Scheme

CSC - Cost-sharing contracts

Coordinator

INSTITUT PASTEUR
Address
Rue du docteur roux 25
75724 Paris
France

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EU contribution
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Participants (7)

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Last update: 31 December 1997

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Permalink: https://cordis.europa.eu/project/id/BIO2942011

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