Plasmids and plasmid modules as orthogonal devices in Synthetic Biology

ESF-UB Conference in Biomedicine

EUROPEAN CONFERENCE ON SYNTHETIC BIOLOGY (ECSB) II: DESIGN, PROGRAMMING AND OPTIMISATION OF BIOLOGICAL SYSTEMS

The field of synthetic biology holds a great promise for the design, construction and development of biological systems (artificial or modified), by offering viable new routes to ‘genetically modified’ organisms, smart drugs and hybrid computational-biological devices. The informed manipulation of such biological systems could have an enormous positive impact on our societies, with its effects being felt across a range of activities such as the provision of healthcare, environmental protection and remediation to the construction of smarter more ubiquitous bio-integrated computing systems, etc.
The basic premise of synthetic biology is that methods commonly used to build non-biological systems, such as those employed in the computational sciences and the engineering disciplines that can deal with large and complex systems, could also be used to specify, design, implement, test and deploy novel synthetic biosystems. Synthetic biology lies at the interface of a variety of disciplines ranging from biology through chemistry, physics, computer science, mathematics and engineering.
Two communities are emerging within synthetic biology, namely top-down - i.e. knocking out or modifying functions of existing cells, and bottom-up - that is construction of artificial systems from first principles, protocells, etc. The aim of this conference is to generate new vigorous interactions between the disciplines that impinge on (and contribute to) Synthetic Biology, and to bring together in the same context top-down and bottom-up researchers.
ECSB 2009 is the second conference in the series. It will comprise invited talks by internationally known scientists who are leaders in their fields, tutorials to introduce young researchers to Synthetic Biology, contributed talks and posters. We expect this to be a major international and multi-disciplinary scientific and educational event. The conference will be limited to just over 100 participants, in a venue whose environment is highly conducive to networking and scientific interactions.
Some, but not all, of the topics to be presented in the conference include: DNA sequencing and synthesis, chemical and biological networks, computational techniques (modelling, data mining, optimisation) for synthetic biology, minimal genomes, evolution (natural, directed and simulated), origins of life, biological systems, cell cycles and circuits, and infrastructures for synthetic biology, minimal cells.

Conference title: Plasmids and plasmid modules as orthogonal devices in Synthetic Biology
Prof. Fernando de la Cruz. Universidad de Cantabria.

http://www.esf.org/activities/esf-conferences/details/2009/confdetail294.html?conf=294&year=2009

The diversity of conjugative relaxases and its application in plasmid classification

The diversity of conjugative relaxases and its application in plasmid classification
María Pilar Garcillán-Barcia 1 , María Victoria Francia 2 & Fernando de la Cruz 1
1 Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-IDICAN, Santander, Spain; and 2 Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla e Instituto de Formación e Investigación Marqués de Valdecilla (IFIMAV), Santander, Spain
Correspondence: Fernando de la Cruz, Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-IDICAN, C. Herrera Oria s/n, 39011 Santander, Spain. Tel.: +34 942201942; fax: +34 942201945; e-mail: delacruz@unican.es
Editor: Eduardo Rocha
Copyright © 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved
KEYWORDS
plasmid classification • relaxase • bacterial conjugation • type IV secretion system • coupling protein
ABSTRACT
Bacterial conjugation is an efficient and sophisticated mechanism of DNA transfer among bacteria. While mobilizable plasmids only encode a minimal MOB machinery that allows them to be transported by other plasmids, conjugative plasmids encode a complete set of transfer genes (MOB+T4SS). The only essential ingredient of the MOB machinery is the relaxase, the protein that initiates and terminates conjugative DNA processing. In this review we compared the sequences and properties of the relaxase proteins contained in gene sequence databases. Proteins were arranged in families and phylogenetic trees constructed from the family alignments. This allowed the classification of conjugative transfer systems in six MOB families: MOBF, MOBH, MOBQ, MOBC, MOBP and MOBV . The main characteristics of each family were reviewed. The phylogenetic relationships of the coupling proteins were also analysed and resulted in phylogenies congruent to those of the cognate relaxases. We propose that the sequences of plasmid relaxases can be used for plasmid classification. We hope our effort will provide researchers with a useful tool for further mining and analysing the plasmid universe both experimentally and in silico.