Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

George C. diCenzo, Alice Checcucci, Marco Bazzicalupo, Alessio Mengoni (), Carlo Viti, Lukasz Dziewit, Turlough M. Finan, Marco Galardini and Marco Fondi
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George C. diCenzo: McMaster University
Alice Checcucci: University of Florence
Marco Bazzicalupo: University of Florence
Alessio Mengoni: University of Florence
Carlo Viti: University of Florence
Lukasz Dziewit: Institute of Microbiology, Faculty of Biology, University of Warsaw
Turlough M. Finan: McMaster University
Marco Galardini: EMBL-EBI, Wellcome Trust Genome Campus
Marco Fondi: University of Florence

Nature Communications, 2016, vol. 7, issue 1, 1-10

Abstract: 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.

Date: 2016
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DOI: 10.1038/ncomms12219

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