Creation and multi-omics characterization of a genomically hybrid strain in the nitrogen-fixing symbiotic bacterium Sinorhizobium meliloti

Checcucci, A.; diCenzo, G. C.; Ghini, V.; Bazzicalupo, M.; Beker, A.; Decorosi, F.; Dohlemann, J.; Fagorzi, C.; Finan, T. M.; Fondi, M.; Luchinat, C.; Turano, P.; Vignolini, T.; Viti, C.; Mengoni, A.

doi:10.1101/296483

bioRxiv · 10.1101/296483

Creation and multi-omics characterization of a genomically hybrid strain in the nitrogen-fixing symbiotic bacterium Sinorhizobium meliloti

Checcucci, A.·diCenzo, G. C.·Ghini, V.·Bazzicalupo, M.·Beker, A.·Decorosi, F.·Dohlemann, J.·Fagorzi, C.·Finan, T. M.·Fondi, M.·Luchinat, C.·Turano, P.·Vignolini, T.·Viti, C.·Mengoni, A.

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Abstract

Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbour a multipartite genome composed by more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extra-cellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modelling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.

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Checcucci, A., diCenzo, G. C., Ghini, V., Bazzicalupo, M., Beker, A., Decorosi, F., Dohlemann, J., Fagorzi, C., Finan, T. M., Fondi, M., Luchinat, C., Turano, P., Vignolini, T., Viti, C., Mengoni, A.. 2018-04-09. Creation and multi-omics characterization of a genomically hybrid strain in the nitrogen-fixing symbiotic bacterium Sinorhizobium meliloti. https://doi.org/10.1101/296483

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