Nature - USA (2020-09-24)

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nature research | reporting summary

October 2018

Data

Policy information about availability of data

All manuscripts must include a data availability statement. This statement should provide the following information, where applicable:

• Accession codes, unique identifiers, or web links for publicly available datasets


• A list of figures that have associated raw data


• A description of any restrictions on data availability
  Data supporting the findings of this work are available within the paper and its Supplementary Information files. The datasets generated and analyzed during the
  current study are available from the corresponding author upon reasonable request. This article includes raw source data files associated with Figs. 1-4 and
  Extended Data Figs. 3, 4, 6 (Supplementary Figure 1), 9, and 10. Novel genetic sequences identified and characterized in this study are available via the following
  accession codes from public databases. 1000Plants (1KP) database: scaffold-AIOU-2012986-Brugmansia_sanguinea (BsUGT); scaffold-JNVS-2051323-Datura_metel
  (DmUGT). Medicinal Plant RNAseq database: medp_datin_20101112|6354 (DiHDH); medp_datst_20101112|10433 (DsHDH). MSU Medicinal Plant Genomics
  Resource: full amino acid sequences and database accession numbers (IDs) for all tested HDH candidates are provided in Supplementary Table 1. Accession
  numbers for previously reported gene and protein sequences in the GenBank/UniProt databases are provided in Supplementary Table 2. Protein crystal structures
  used for homology modeling are available from the RCSB protein data bank: Arabidopsis thaliana salicylate UDP-glucosyltransferase UGT74F2 with bound UDP, PDB:
  5V2K; Populus tremuloides sinapyl alcohol dehydrogenase with bound NADPH, PDB: 1YQD. The custom R script used for identification of HDH candidates via
  coexpression analysis of RNA sequencing data is available from the Smolke Laboratory GitHub: github.com/smolkelab/Oxidoreductase_coexpression_analysis.

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Life sciences study design

All studies must disclose on these points even when the disclosure is negative.

Sample size All presented titer data represent measurements from sample sizes of n = 3 biological replicates, where biological replicates (as defined in

'Replication' below) represent independently grown microbial cultures. Since (i) engineering was performed at the cellular level, (ii)

metabolite titers are a bulk measure of a cellular population, and (iii) each assayed microbial culture represents a large population of

individual cells, n = 3 biological replicates were chosen as they are sufficient for reliable measurement of changes in metabolite production at

the population level and for statistical analyses, based on previous metabolic engineering papers.

Data exclusions No data were excluded from the analyses.

Replication All measurements of metabolite titers were performed on n = 3 biologically independent samples (biological triplicates). All replicates

performed in this study were biological replicates, rather than technical replicates, and represent independent data points. For example,

replicate microbial cultures were grown in separate containers/wells and assayed independently from one another. Fluorescence microscopy

and Western blot analyses shown in the paper are representative of two or three independent experiments; all attempts at replication of

results presented in this study were successful.

Randomization Randomization of individual cells was not relevant to this study, as the biological subjects for assays were bulk cultures of microbial cells.

Microbial strains used for all experiments were inoculated from randomly selected colonies on agar plates. Representative fields of view were

selected randomly for fluorescence microscopy.

Blinding Complete blinding was not feasible for this study, as samples were prepared and measured by the same researcher. However, all samples

were labeled with numeric codes, rather than names or descriptions, throughout the sample preparation and data collection work-flow to

simulate blinding.

Reporting for specific materials, systems and methods

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system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.