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The Biology and Physics of Bacterial Genome Organization
Description and aims
Defining the compaction and functional organization of genomes is a question of longstanding biological interest in bacteria as well as in other organisms. Nevertheless, we remain far from an integrated model that describes the interactions that organize the bacterial nucleoid. A key tenet of the workshop was that understanding chromosome structure and function requires knowledge spanning different “length scales”. On the nanometer scale, the configuration of the DNA is modulated by the action of small chromatin proteins. At an intermediate scale, the genome has been proposed to fold into loops on the order of 10 kbp in size. On the micrometer scale, genomes are divided into independently structured domains on the order of 1 Mbp in size. An interconnecting model describing all of these length scales remains elusive. Aim of the workshop was to bring together people from diverse disciplinary backgrounds to facilitate generating and bridging knowledge on different length scales.
During the last decade numerous researchers, applying novel methodology have entered the field of bacterial genome organization. Thus the study of bacterial chromosomes is in a stage of revival and novel excitement. The workshop gathered about 55 scholars with diverse disciplinary backgrounds and both experimental and theoretical approaches (including but not limited to (micro)biology, (bio)chemistry, bioinformatics, cell biology, polymer physics). The workshop was thematically organized around the three different levels of organization mentioned above. Thus, the participants in this workshop ventured into a multidisciplinary journey to explore different levels of organization.
Many of the participants had not met before. Bringing people of diverse backgrounds together and promote interaction was one of the key aims achieved by the meeting. An important conclusion was that the nucleoid is a dynamic entity, that its components interact with each other differentially over time and that these interactions are encoded within the genome itself. This notion underscores the importance of approaches that are capable of addressing and integrating these different aspects. It seems a feasible issue to tackle for the community present at the workshop and first steps in this direction were indeed already taken. It also brings to the light aspects that were not or hardly addressed by participants during this meeting. For instance, what is the interplay of genome folding with replication? How does the structure of the genome affect damage induction, repair and mutagenesis and vice versa? What role does genome folding play in evolution, incorporation of foreign DNA by horizontal gene transfer etc? Finally, it is fair to conclude that bringing together people from different fields at a meeting like this is not enough. No doubt the workshop has been able to generate more openness to (and understanding of) the types of data generated by the diverse approaches. However, at this stage it is hard to integrate much of the available data as the experimental conditions are so widely different. Clearly new collaborative efforts are required especially in order to compare and integrate data from superresolution imaging, ChIP and 3C. A next workshop, to be organized in two or three years, will show the outcome of newly established collaborations and hopefully address many of the outstanding questions.
The most important new findings and outcomes of the interdisciplinary interactions during the workshop were compiled in a meeting report “Multidisciplinary perspectives on bacterial genome organization and dynamics“ published by Molecular Microbiology (Dame et al., 2012).
Format of the workshop
The workshop was organized by length scale. Every day a different length scale relevant to the problem was the topic of presentations by speakers. Both the morning and the afternoon sessions were followed by guided discussions of points raised by speakers and participants. On day 5 the most important points were collected and once more discussed from the perspective of knowledge integration. Generally, this format worked well and many of the participants were involved in the discussions. Key to this was the selection of expert chairs for these sessions. In addition to oral presentations we organized a poster session, which served well in people meeting each other and we had long lunch breaks to facilitate ad hoc interactions. Overall, this generated a pleasant, friendly and open atmosphere in which people were freely interacting.
The authors thank all meeting participants for their excellent contributions and the Lorentz Center staff for their superb planning and organization.
Remus T. Dame (Leiden University, The Netherlands)
Olivier Espéli (CNRS, Gif-sur-Yvette, France)
David C. Grainger (University of Birmingham, UK)
Paul A. Wiggins (University of Washington, USA)