title: Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti.
abstract: The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental adaptations and/or niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological niches and an overall reprogramming following niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated niche adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes.
authors.affiliation: Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 1A1.
authors.forename: George C
authors.initials: GC
authors.lastname: diCenzo
authors.affiliation: Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy.
authors.forename: Alice
authors.initials: A
authors.lastname: Checcucci
authors.affiliation: Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Bazzicalupo
authors.affiliation: Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy.
authors.forename: Alessio
authors.identifier: 0000-0002-1265-8251
authors.initials: A
authors.lastname: Mengoni
authors.affiliation: Department of Agri-food Production and Environmental Sciences, University of Florence, 50144 Sesto Fiorentino, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Viti
authors.affiliation: Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland.
authors.forename: Lukasz
authors.initials: L
authors.lastname: Dziewit
authors.affiliation: Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 1A1.
authors.forename: Turlough M
authors.initials: TM
authors.lastname: Finan
authors.affiliation: EMBL-EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.
authors.forename: Marco
authors.identifier: 0000-0003-2018-8242
authors.initials: M
authors.lastname: Galardini
authors.affiliation: Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Fondi
mesh_terms: D000222:Adaptation, Physiological / Q000187:drug effects; D002244:Carbon / Q000494:pharmacology; D003198:Computer Simulation; D017753:Ecosystem; D017353:Gene Deletion; D056084:Genetic Fitness; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways / Q000187:drug effects; D008954:Models, Biological; D010641:Phenotype; D012093:Replicon / Q000235:genetics*; D015203:Reproducibility of Results; D058441:Rhizosphere; D016962:Sinorhizobium meliloti / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D012987:Soil / Q000737:chemistry; D013559:Symbiosis
chemical_list: D012987:Soil; D002244:Carbon