Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbour a multipartite genome composed of 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. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species' pangenome. 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.

Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti / Checcucci, Alice; diCenzo, George; Ghini, Veronica; Bazzicalupo, Marco; Becker, Anke; Decorosi, Francesca; Döhlemann, Johannes; Fagorzi, Camilla; Finan, Turlough M; Fondi, Marco; Luchinat, Claudio; Turano, Paola; Vignolini, Tiziano; Viti, Carlo; Mengoni, Alessio. - In: ACS SYNTHETIC BIOLOGY. - ISSN 2161-5063. - STAMPA. - 7:(2018), pp. 2365-2378. [10.1021/acssynbio.8b00158]

Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti

Checcucci, Alice;Ghini, Veronica;Bazzicalupo, Marco;Decorosi, Francesca;Fagorzi, Camilla;Fondi, Marco;Luchinat, Claudio;Turano, Paola;VIGNOLINI, TIZIANO;Viti, Carlo;Mengoni, Alessio
2018

Abstract

Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbour a multipartite genome composed of 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. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species' pangenome. 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.
2018
7
2365
2378
Checcucci, Alice; diCenzo, George; Ghini, Veronica; Bazzicalupo, Marco; Becker, Anke; Decorosi, Francesca; Döhlemann, Johannes; Fagorzi, Camilla; Finan, Turlough M; Fondi, Marco; Luchinat, Claudio; Turano, Paola; Vignolini, Tiziano; Viti, Carlo; Mengoni, Alessio
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Descrizione: Checcucci et al. 2018 ACS SynthBiol
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Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/1136061
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