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Investigation of secondary metabolism in the industrial butanol hyper-producer Clostridium saccharoperbutylacetonicum N1-4

Abstract

Clostridium saccharoperbutylacetonicum N1-4 (Csa) is a historically significant anaerobic bacterium which can perform saccharolytic fermentations to produce acetone, butanol, and ethanol (ABE). Recent genomic analyses have highlighted this organism’s potential to produce polyketide and nonribosomal peptide secondary metabolites, but little is known regarding the identity and function of these metabolites. This study provides a detailed bioinformatic analysis of seven biosynthetic gene clusters (BGCs) present in the Csa genome that are predicted to produce polyketides/nonribosomal peptides. An RNA-seq-based untargeted transcriptomic approach revealed that five of seven BGCs were expressed during ABE fermentation. Additional characterization of a highly expressed nonribosomal peptide synthetase gene led to the discovery of its associated metabolite and its biosynthetic pathway. Transcriptomic analysis suggested an association of this nonribosomal peptide synthetase gene with butanol tolerance, which was supported by butanol challenge assays.

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Acknowledgements

We thank J. Pelton (UC Berkeley) for helping with NMR spectroscopic analysis, the University of California-Berkeley QB3 Functional Genomics Laboratory and Vincent J. Coates Genomic Sequencing Laboratory for performing the RNA-Seq library preparation and sequencing. This work was financially supported by the Energy Biosciences Institute, Alfred P. Sloan Foundation, and the National Institutes of Health (DP2AT009148).

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Li, J.S., Barber, C.C., Herman, N.A. et al. Investigation of secondary metabolism in the industrial butanol hyper-producer Clostridium saccharoperbutylacetonicum N1-4. J Ind Microbiol Biotechnol 47, 319–328 (2020). https://doi.org/10.1007/s10295-020-02266-8

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Keywords

  • Anaerobe
  • ABE fermentation
  • Polyketide synthase
  • Nonribosomal peptide synthetase
  • Transcriptomics