Universal and idiosyncratic characteristic lengths in bacterial genomes
| Autor: | Olivier Rivoire, Ivan Junier, Paul Frémont |
|---|---|
| Přispěvatelé: | Génomique et Évolution des Microorganismes (TIMC-IMAG-GEM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM) |
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
MESH: Chromosomes Bacterial MESH: Sequence Analysis DNA Characteristic length Base pair Biophysics Bacterial genome size MESH: Genome Bacterial Synteny Genome Evolution Molecular 03 medical and health sciences 0302 clinical medicine MESH: Base Composition Structural Biology Kuhn length Quantitative Biology - Genomics Molecular Biology MESH: Evolution Molecular Genomics (q-bio.GN) Base Composition Bacteria Circular bacterial chromosome [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] MESH: Synteny Sequence Analysis DNA Cell Biology Chromosomes Bacterial MESH: Bacteria 030104 developmental biology Evolutionary biology FOS: Biological sciences Genome Bacterial 030217 neurology & neurosurgery GC-content |
| Zdroj: | Physical Biology Physical Biology, Institute of Physics: Hybrid Open Access, 2018, 15 (3), pp.035001. ⟨10.1088/1478-3975/aab4ac⟩ |
| ISSN: | 1478-3967 1478-3975 |
| Popis: | International audience; In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a physics standpoint, in vitro DNA has thus a characteristic length of 300 base pairs (bp), the Kuhn length of the molecule beyond which correlations in its orientations are typically lost. From a biology standpoint, in vivo DNA has a characteristic length of 1000 bp, the typical length of genes. Since bacteria live in very different physico-chemical conditions and since their genomes lack translational invariance, whether larger, universal characteristic lengths exist is a non-trivial question. Here, we examine this problem by leveraging the large number of fully sequenced genomes available in public databases. By analyzing GC content correlations and the evolutionary conservation of gene contexts (synteny) in hundreds of bacterial chromosomes, we conclude that a fundamental characteristic length around 10-20 kb can be defined. This characteristic length reflects elementary structures involved in the coordination of gene expression, which are present all along the genome of nearly all bacteria. Technically, reaching this conclusion required us to implement methods that are insensitive to the presence of large idiosyncratic genomic features, which may co-exist along these fundamental universal structures. |
| Databáze: | OpenAIRE |
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