Genetics of Bacterial Genomes - CNRS URA2171  

  HEADAntoine Danchin /
  MEMBERSJean-François Charles, Dr. / Anne-Marie Gilles, Dr. / Evelyne Turlin, Ingénieur / Jérémie Loyau, Stagiaire / Sabina Chalabaev, Thèse / Emma Brito-Fravalo, Technicienne
Marie-Françoise Hullo, Ingénieur / Evelyne Krin, Ingénieur, / Olga Soutourina, Dr. / Isabelle Martin-Verstraete, Prof. / Gaëlle André, Thèse / Marie-Pierre Fourquin, Thèse / Catherine Tanous, Dr. / Emmanuelle Courtois, Technicienne
Undine Mechold, Dr. / Arnaud Gutierrez, Stagiaire / Conghui You, Thèse, puis Dr.
Tingzhang Wang, Thèse / Sandra Cescau, Dr. / Jean-Baptiste Masson, Dr. / Anne-Sophie Peysson, Secrétaire / (localisation hors IP : Eduardo Rocha, Dr., Marie Touchon, Dr.)

  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 living computer, and if so, what are the implications in terms of the concrete biological objects that make it run ? The accidents of replication 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 silico, 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 programs, 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. Genes that persist in bacterial genomes cluster together, and we showed that being persistent provides enough power for creating clusters in genomes that are permanently witnessing fluxes of genes going in and out.

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 organisation. This led us to discover univerals in the composition of proteins, and to propose that aromatic-rich orphan genes code for proteins that stabilise 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 Bacteria to Humans. This will undoubtledly have interesting consequences in terms of RNA metabolism, recently recognized as of prime importance for genetic and epigenetic heredity. This experimental work validates the observation in silico that persistent genes keep being organized in bacterial genomes along a pattern that is reminiscent of a scenario of the origin of life beginning with surface metabolism, making the « paleome » which opposed to genes allowing life in context, making the « cenome ».

Keywords: biologie synthétique / origine de la vie / évolution / métabolisme du soufre / bactéries entomopathogènes / nucléotides / génomique comparative /synbthetic biology / origin of life / evolution / sulfur metabolism / insect pathogens / nucleotides / comparative genomics


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


A Sekowska, V Dénervaud, H Ashida, K Michoud, D Haas, A Yokota, A Danchin. Bacterial variations on the methionine salvage pathway BMC Microbiol(2004) 4:9

G Fang, EPC Rocha, A Danchin. How essential are non-essential genes? Mol Biol Evol(2005) 22: 2147-2156

C Médigue, E Krin, G Pascal, V Barbe, A Bernsel, PN Bertin, F Cheung, S Cruveiller, S D'Amico, A Duilio, G Fang, G Feller, C Ho, S Mangenot, G Marino, J Nilsson, E Parrilli, EPC Rocha, Z Rouy, A Sekowska, ML Tutino, D Vallenet, G von Heijne, A Danchin. Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktisTAC125

Genome Res(2005) 15: 1325-1335

MF Hullo, S Auger, O Soutourina, O, Barzu, M Yvon, A Danchin, I Martin-Verstraete. The conversion of methionine to cysteine in Bacillus subtilis and its regulation.J Bacteriol(2007) 189: 187-197

A Danchin, G Fang, S Noria. The extant core bacterial proteome is an archive of the origin of life. Proteomics(2007) 7:875-889

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Activity Reports 2007 - Institut Pasteur
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