title: The layout of a bacterial genome.
abstract: Recently the mismatch between our newly acquired capacity to synthetize DNA at genome scale, and our low capacity to design ab initio a functional genome has become conspicuous. This essay gathers a variety of constraints that globally shape natural genomes, with a focus on eubacteria. These constraints originate from chromosome replication (leading/lagging strand asymmetry; gene dosage gradient from origin to terminus; collisions with the transcription complexes), from biased codon usage, from noise control in gene expression, and from genome layout for co-functional genes. On the basis of this analysis, lessons are drawn for full genome design.
authors.affiliation: Epigenomics Project, Institute of Systems and Synthetic Biology, CNRS, University of Evry, France. francois.kepes@epigenomique.genopole.fr
authors.forename: François
authors.initials: F
authors.lastname: Képès
authors.forename: Brian C
authors.initials: BC
authors.lastname: Jester
authors.forename: Thibaut
authors.initials: T
authors.lastname: Lepage
authors.forename: Nafiseh
authors.initials: N
authors.lastname: Rafiei
authors.forename: Bianca
authors.initials: B
authors.lastname: Rosu
authors.forename: Ivan
authors.initials: I
authors.lastname: Junier
mesh_terms: D001419:Bacteria / Q000235:genetics*; D002876:Chromosomes, Bacterial / Q000235:genetics; D018628:Gene Dosage / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D058615:Synthetic Biology / Q000379:methods*