title: Evolvability and hierarchy in rewired bacterial gene networks.
abstract: Sequencing DNA from several organisms has revealed that duplication and drift of existing genes have primarily moulded the contents of a given genome. Though the effect of knocking out or overexpressing a particular gene has been studied in many organisms, no study has systematically explored the effect of adding new links in a biological network. To explore network evolvability, we constructed 598 recombinations of promoters (including regulatory regions) with different transcription or sigma-factor genes in Escherichia coli, added over a wild-type genetic background. Here we show that approximately 95% of new networks are tolerated by the bacteria, that very few alter growth, and that expression level correlates with factor position in the wild-type network hierarchy. Most importantly, we find that certain networks consistently survive over the wild type under various selection pressures. Therefore new links in the network are rarely a barrier for evolution and can even confer a fitness advantage.
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), UPF, 08003 Barcelona, Spain. isalan@crg.es
authors.forename: Mark
authors.initials: M
authors.lastname: Isalan
authors.forename: Caroline
authors.initials: C
authors.lastname: Lemerle
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Michalodimitrakis
authors.forename: Carsten
authors.initials: C
authors.lastname: Horn
authors.forename: Pedro
authors.initials: P
authors.lastname: Beltrao
authors.forename: Emanuele
authors.initials: E
authors.lastname: Raineri
authors.forename: Mireia
authors.initials: M
authors.lastname: Garriga-Canut
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
mesh_terms: D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics; D005818:Genetic Engineering; D018869:Heat-Shock Response; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D012641:Selection, Genetic; D012692:Serial Passage; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; D012808:Sigma Factor; D014157:Transcription Factors