In vitro and in vivo characterization of a new-to-nature pathway for formaldehyde assimilation in methylotrophic yeast Komagataella phaffii

This repository contains the raw data, processed data used for analysis, and the scripts for generating the figures and tables presented in the manuscript, In vitro and in vivo characterization of a new-to-nature pathway for formaldehyde assimilation in methylotrophic yeast Komagataella phaffii.

Fig 2. A was visualized from the data files "Chi.Bio_FLS pool (MeOH).xlsx" and "Chi.Bio_XuMP– (MeOH).xlsx".  Fig 2. B was visualized from the data file "Chi.Bio_FLS pool (MeOH+DHA).xlsx". Fig 2. C was visualized from the data file "Chi.Bio_XuMP– (MeOH+DHA).xlsx". Fig 2. D was visualized from the data files "Chi.Bio_FLS pool (MeOH+DHA).xlsx" and "Chi.Bio_XuMP– (MeOH+DHA).xlsx".

Fig 3. D was visualized from the data file "LC_MS_DHA_R.xlsx" and using the R script "DHA measurement and visualization (Fig. 3D)". Fig 3. E was visualized from the data file "LC_MS_GALD_R.xlsx" and using the R script "GALD measurement and visualization (Fig. 3E)".

Fig 4. A, B, C, D, E, and F were visualized from the data files "AOX1.csv", "AOX2.csv", "FLS.csv", "DAS1.csv", "DAS2.csv" "DAK2.csv", respectively and using the Python script "Protein intensities from proteomics data (Fig 4. A, B, C, D, E, F)".

Fig 5. A was calculated and visualized from the data file "DASGIP_DATAFILE_RS.xlsx" and using the R script "DASGIP2 DCW visualization (Fig 5. A)". Fig 5. B was calculated and visualized from the data file "MeOHCon.xlsx" using the R script "DASGIP2 MeOH visualization (Fig. 5. B)". Fig 5. C was calculated and visualized from the data file "MeOH.xlsx" and using the R script "DASGIP2 MeOH visualization (Fig. 5. C)". Table 2 is calculated from the raw data in the file "DASGIP_DATAFILE_RS.xlsx".csv".

Table 2 was calculated from the raw data in the file "DASGIP_DATAFILE_RS.xlsx".csv".

Fig S2 was calculated and visualized from the data file "Kphaffiiproteom.xlsx" and using the R script "PCA analysis of proteomics data (Fig. S1)". Fig S3 was calculated and visualized from the data file "Proteomics_strains_log2_FC.csv" and using the Python script "Proteomics_Log2FC_AdjPvalue_Volcano plot". Table S7 was calculated from the raw data in the file "43_K_phaffi_proteome_analysis.xlsx". 

Note: This is an updated version of the previous one. Some files not mentioned in the publication have been removed, and new data, mainly on Chi.Bio cultivation has been added.