Genetics of Bacterial Genomes - CNRS URA2171  


  HEADProf. DANCHIN Antoine / adanchin@pasteur.fr
  MEMBERSDr CHARLES Jean-François / Dr GANG Fang / Dr GILLES Anne-Marie
HULLO Marie-Françoise / KRIN Evelyne / Prof. MARTIN-VERSTRAETE Isabelle
Dr MECHOLD Undine / Dr PIMENTEL CACHAPUZ Eduardo
Dr SOUTOURINA Olga / Dr TOUCHON Marie / TURLIN Evelyne


  Annual Report

John von Neumann showed that for a computer to make a computer it needs that there is an image of the machine within, passed along from generation to generation. Pushing the genetic program metaphor to its limits, this reflection underlies our research: is it possible to view the cell as a Turing machine, and if so, what are the implications in terms of concrete biological objects needed to make it run. The accidents of reproduction lead genes to be modified, to disappear or to change place. One expects to observe that they rapidly distribute more or less randomly. Is the order of the genes random? Where are located the gene products, does one find them everywhere? Our work explored this conjecture, with experiments meant to uncover some of the physico-chemical constraints organizing the cell. To this aim, experimental work is combined with work in , conceptual investigations serving as references and predictions for experiments.

Gene “persistence”. As a start point, we analyzed how DNA and genes are handled by the various machineries in bacteria, explored the diversity of the corresponding processes and looked for common features. We further explored bacterial genome diversity to find out the nature of processes imbedded in the genetic programmes, to understand what makes both their universal nature and their diversity. The core of our approach explores the relationships between biological objects, trying to relate the architecture of the genome to that of the cell. We observed that genes that persist in bacterial genomes, form consistent functional categories, and are clustered together.

Universal biases in the composition of proteins: the “gluon” hypothesis. Having shown that the codon usage bias, the chromosome strand preference, the expressivity and the essentiality of genes all cooperate to shape genomes, we looked for selection pressures that may drive that organization. This led us to discover universals in the composition of proteins, and to propose that aromatic-rich orphan genes code for proteins that stabilize complexes (“gluons”).

Sulfur metabolism: anabolism, salvage and control of “nanoRNA” degradation. We chose to focus on two such constrains: temperature and reactivity of the sulfur atom, and we tested our interpretation of the data we collect on pathogenicity as an integrating process. While we uncovered many new features of sulfur metabolism we discovered that a side-product of sulfur assimilation, 3’5’AMP, is a regulator of very small RNA degradation, in a pathway that seems to extend from Proteobacteria to Humans. This will undoubtedly have interesting consequences in terms of RNA metabolism, recently recognized as of prime importance for genetic and epigenetic heredity.

danchin.jpg

Analyse Factorielle des Correspondances du protéome d’une bactérie psychrophile montrant un biais dans l’abondance de l’asparagine, acide aminé « vieillissant » rapidement.

Correspondence Analysis of a psychrophilic bacterium proteome showing a bias for asparagine, a rapidly “aging” amino acid.



  Publications

Publications 2006 of the unit on Pasteur's references database




Activity Reports 2006 - Institut Pasteur
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