, 12:23 | Cite as

Effects of synthetic large-scale genome reduction on metabolism and metabolic preferences in a nutritionally complex environment

  • Fan Fei
  • George C. diCenzo
  • Dawn M. E. Bowdish
  • Brian E. McCarry
  • Turlough M. Finan
Original Article


The soil bacterium Sinorhizobium meliloti forms nodules on the roots of leguminous plants, where N2 is reduced to ammonia. Its genome includes a 3.65 Mb chromosome, a 1.35 Mb pSymA megaplasmid, and a 1.68 Mb pSymB chromid. pSymA and pSymB constitute ~45 % of the genome and here a non-targeted approach was used to identify the metabolic consequences of the removal of these replicons. Polar and non-polar metabolites from wild-type, ∆pSymA, ∆pSymB, and ∆pSymAB cells and supernatants across a growth curve were analyzed by LC–HILIC–TOF–MS. 2008 metabolite features were identified in the extracellular metabolome of cells grown in LBmc containing yeast extract and casein hydrolysate. 1474 features were found from the intracellular metabolites of cells grown in minimal M9-sucrose medium. Analysis revealed both time and genotype influenced the metabolome, with the removal of pSymB having a much greater effect than the loss of pSymA. Strains lacking pSymB showed an increase in sugar, amino acid, and nucleotide metabolites in the intracellular metabolome, and the loss of pSymB clearly impaired the cell’s ability to catabolize exogenous amino acids. We conclude that despite the ability of wild-type, ∆pSymA, ∆pSymB, and ∆pSymAB strains to grow in both M9-sucrose and LBmc media, the removal of pSymA, and particularly pSymB, had clear and dramatic effects on the S. meliloti metabolome. The larger effect associated with the pSymB chromid is consistent with the large number of metabolic genes on this replicon and the greater genetic and metabolic integration of this replicon with the S. meliloti chromosome.


Sinorhizobium Metabolism Multipartite Microbial 



This work is dedicated to the late Prof. Brian McCarry (1946–2013). Funding for this work was provided by NSERC to B. E. M. and T. M. F. The authors would like to thank the Center for Microbial Chemical Biology (CMCB) at McMaster for access to the LC–MS. F. F. is supported by an Ontario Graduate Scholarship and G. C. D by a NSERC CGS award.

Compliance with ethical standards

Conflict of interest

Authors Fan Fei, George C. diCenzo, Dawn M. E. Bowdish, Brian E. McCarry (deceased), and Turlough M. Finan declare that they have no conflict of interest.

Ethical Approval

This work did not involve human particpants and/or animals, and all authors have agreed to submission of the manuscript.

Supplementary material

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Supplementary material 1 (PDF 1685 kb)
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Supplementary material 2 (XLSX 2037 kb)
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Supplementary material 3 (XLSX 2056 kb)


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Fan Fei
    • 1
  • George C. diCenzo
    • 2
  • Dawn M. E. Bowdish
    • 3
  • Brian E. McCarry
    • 1
  • Turlough M. Finan
    • 2
  1. 1.Department of Chemistry and Chemical BiologyMcMaster UniversityHamiltonCanada
  2. 2.Department of BiologyMcMaster UniversityHamiltonCanada
  3. 3.Department of Pathology and Molecular Medicine, Michael G. DeGroote Institute for Infectious Disease ResearchMcMaster UniversityHamiltonCanada

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