Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast

Nucleic Acids Res. 2020 Jan 10;48(1):486-499. doi: 10.1093/nar/gkz1098.


Cross-species pathway transplantation enables insight into a biological process not possible through traditional approaches. We replaced the enzymes catalyzing the entire Saccharomyces cerevisiae adenine de novo biosynthesis pathway with the human pathway. While the 'humanized' yeast grew in the absence of adenine, it did so poorly. Dissection of the phenotype revealed that PPAT, the human ortholog of ADE4, showed only partial function whereas all other genes complemented fully. Suppressor analysis revealed other pathways that play a role in adenine de-novo pathway regulation. Phylogenetic analysis pointed to adaptations of enzyme regulation to endogenous metabolite level 'setpoints' in diverse organisms. Using DNA shuffling, we isolated specific amino acids combinations that stabilize the human protein in yeast. Thus, using adenine de novo biosynthesis as a proof of concept, we suggest that the engineering methods used in this study as well as the debugging strategies can be utilized to transplant metabolic pathway from any origin into yeast.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenine / biosynthesis*
  • Amino Acid Sequence
  • Biosynthetic Pathways / genetics*
  • CRISPR-Cas Systems
  • Carboxy-Lyases / genetics*
  • Carboxy-Lyases / metabolism
  • Chromosomes, Artificial, Human / chemistry*
  • Chromosomes, Artificial, Human / metabolism
  • Genetic Complementation Test
  • Genetic Engineering / methods
  • Humans
  • Isoenzymes / genetics
  • Isoenzymes / metabolism
  • Peptide Synthases / genetics*
  • Peptide Synthases / metabolism
  • Phylogeny
  • Plasmids / chemistry
  • Plasmids / metabolism
  • Saccharomyces cerevisiae / classification
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Sequence Alignment
  • Sequence Homology, Amino Acid


  • Isoenzymes
  • Carboxy-Lyases
  • Peptide Synthases
  • Adenine