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Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains

Nature Biotechnology volume 21, pages 150–156 (2003)Cite this article

Abstract

We describe a method to decipher the complex inter-relationships between metabolite production trends and gene expression events, and show how information gleaned from such studies can be applied to yield improved production strains. Genomic fragment microarrays were constructed for the Aspergillus terreus genome, and transcriptional profiles were generated from strains engineered to produce varying amounts of the medically significant natural product lovastatin. Metabolite detection methods were employed to quantify the polyketide-derived secondary metabolites lovastatin and (+)-geodin in broths from fermentations of the same strains. Association analysis of the resulting transcriptional and metabolic data sets provides mechanistic insight into the genetic and physiological control of lovastatin and (+)-geodin biosynthesis, and identifies novel components involved in the production of (+)-geodin, as well as other secondary metabolites. Furthermore, this analysis identifies specific tools, including promoters for reporter-based selection systems, that we employed to improve lovastatin production by A. terreus.

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Figure 1: Characterization of metabolic and transcriptional diversity.
Figure 2: Selection systems identify improved strains.

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Acknowledgements

We are grateful to Brian Cali, Gerry Fink, and Todd Milne for critical comments on this manuscript. In addition, the authors would like to thank all members of the Precision Engineering program at Microbia, Inc. for their support and helpful discussions.

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Author notes

  1. Manor Askenazi and Edward M. Driggers: These authors contributed equally to this work.

Authors and Affiliations

  1. Microbia, Inc., 320 Bent Street, Cambridge, 02141, MA

    Manor Askenazi, Edward M. Driggers, Douglas A. Holtzman, Thea C. Norman, Sara Iverson, Daniel P. Zimmer, Mary-Ellen Boers, Paul R. Blomquist, Eduardo J. Martinez, Alex W. Monreal, Toby P. Feibelman, Maria E. Mayorga, Kristie Sykes, Jenny Vittum Tobin, Etchell Cordero, Joshua Trueheart, John C. Royer & Kevin T. Madden

  2. Cytokinetics, Inc., 280 East Grand Ave., Suite 2, S., San Francisco, 94080, CA

    Mary E. Maxon

  3. University of California, Santa Cruz, Jack Baskin Engineering Bldg., 1156 High St., Santa Cruz, 95064, CA

    Sofie R. Salama

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Correspondence to Kevin T. Madden.

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Competing interests

This work was supported by Microbia, Inc. All authors are or have been employed by Microbia, Inc., and the authors have had the option to become shareholders in the company. The authors declare that a patent application has been filed that relates to the content of this manuscript.

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Askenazi, M., Driggers, E., Holtzman, D. et al. Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nat Biotechnol 21, 150–156 (2003). https://doi.org/10.1038/nbt781

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