Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic BacteriumSinorhizobium meliloti Academic Article uri icon

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abstract

  • Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor 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 extracellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modeling 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.

authors

  • Checcucci, Alice
  • diCenzo, George C
  • Ghini, Veronica
  • Bazzicalupo, Marco
  • Becker, Anke
  • Decorosi, Francesca
  • Döhlemann, Johannes
  • Fagorzi, Camilla
  • Finan, Turlough Mary
  • Fondi, Marco
  • Luchinat, Claudio
  • Turano, Paola
  • Vignolini, Tiziano
  • Viti, Carlo
  • Mengoni, Alessio

publication date

  • October 19, 2018