Resurrecting essential amino acid biosynthesis in a mammalian cell

Trolle, J.; McBee, R. M.; Kaufman, A.; Pinglay, S.; Berger, H.; German, S.; Liu, L.; Shen, M. J.; Guo, X.; Martin, J. A.; Pacold, M.; Jones, D. R.; Boeke, J. D.; Wang, H. H.

doi:10.1101/2021.08.03.454854

bioRxiv · 10.1101/2021.08.03.454854

Resurrecting essential amino acid biosynthesis in a mammalian cell

Trolle, J.·McBee, R. M.·Kaufman, A.·Pinglay, S.·Berger, H.·German, S.·Liu, L.·Shen, M. J.·Guo, X.·Martin, J. A.·Pacold, M.·Jones, D. R.·Boeke, J. D.·Wang, H. H.

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Abstract

Major genomic deletions in independent eukaryotic lineages have led to repeated ancestral loss of biosynthesis pathways for nine of the twenty canonical amino acids1. While the evolutionary forces driving these polyphyletic deletion events are not well understood, the consequence is that extant metazoans are unable to produce nine essential amino acids (EAAs). Previous studies have highlighted that EAA biosynthesis tends to be more energetically costly2,3, raising the possibility that these pathways were lost from organisms with access to abundant EAAs in the environment4,5. It is unclear whether present-day metazoans can reaccept these pathways to resurrect biosynthetic capabilities that were lost long ago or whether evolution has rendered EAA pathways incompatible with metazoan metabolism. Here, we report progress on a large-scale synthetic genomics effort to reestablish EAA biosynthetic functionality in a mammalian cell. We designed codon-optimized biosynthesis pathways based on genes mined from Escherichia coli. These pathways were de novo synthesized in 3 kilobase chunks, assembled in yeasto and genomically integrated into a Chinese Hamster Ovary (CHO) cell line. One synthetic pathway produced valine at a sufficient level for cell viability and proliferation, and thus represents a successful example of metazoan EAA biosynthesis restoration. This prototrophic CHO line grows in valine-free medium, and metabolomics using labeled precursors verified de novo biosynthesis of valine. RNA-seq profiling of the valine prototrophic CHO line showed that the synthetic pathway minimally disrupted the cellular transcriptome. Furthermore, valine prototrophic cells exhibited transcriptional signatures associated with rescue from nutritional starvation. This work demonstrates that mammalian metabolism is amenable to restoration of ancient core pathways, thus paving a path for genome-scale efforts to synthetically restore metabolic functions to the metazoan lineage.

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Trolle, J., McBee, R. M., Kaufman, A., Pinglay, S., Berger, H., German, S., Liu, L., Shen, M. J., Guo, X., Martin, J. A., Pacold, M., Jones, D. R., Boeke, J. D., Wang, H. H.. 2021-08-03. Resurrecting essential amino acid biosynthesis in a mammalian cell. https://doi.org/10.1101/2021.08.03.454854

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