teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering
Fig 2
Design and characteristics of the constituent DNA parts used as experimental testbed for teemi.
(A) The ten-step biosynthetic pathway converting geraniol to strictosidine. The G8H step is highlighted in a dashed box [26]. (B-C) Rooted phylogenetic trees of G8H (D) and CPR (E) protein representatives. Uniprot identifiers are shown in parentheses. Catharanthus roseus (Cro), Rauvolfia serpentina (Rse), Olea europaea (Oeu), Camptotheca acuminata (Cac), Vinca minor (Vmi), Cinchona calisaya (Cca), Ophiarrhiza pumila (Opu), and Swertia mussatii (Smu), Artemisia annua (Aan), Arabidopsis thaliana (Ath), Catharanthus longifolius (Clo), Amsania hubrichtii (Ahu), and Aspergillus niger (Ani). (D-E) Temporal resolution of transcript abundances for candidate genes [34], for which promoters were chosen to control the expression of genes encoding G8H (D) and CPR (D) homologous. (F) Combinatorial assembly and genome integration strategy.