Fig. 7: Proteomics analysis of SM7 and SM1.

a Abundance ratio of the 44 E. coli ribosomal subunit proteins in SM7, SM1 (grown in 400 mM methanol), and wild-type parental strain BW25113 (grown in 1% glucose). The boxplot is generated with their whiskers defining the maximum and minimum value, while the box encloses the first (25%) and third (75%) quartiles, with an additional line at the second quartile marking the median. Error bars represent SD. b Functional enrichment analysis identified biological processes by comparing SM7 to SM1 grown with 400 mM methanol until OD₆₀₀ reached 1. The gene ratio on the x-axis represents the proportion of genes from a given gene set that are found to be differentially expressed or enriched in the analyzed dataset. A higher gene ratio indicates that a larger proportion of the gene set is involved in the indicated biological pathway. The adjusted P-value with Benjamini-Hochberg Procedure are shown with the color code (p. adjust). The data is generated by using GSEA with a permutation-based two-tailed test with 1000 permutations, with a FDR calculated P-value of 0.05 cutoff. c Metabolic protein abundance ratios. The left and right boxes represent SM7/WT and SM1/WT log₂ ratios, respectively. The circles represent the log₂ ratios of SM7/SM1 non-native proteins (Mdh, Hps, and Phi). Hps was cloned from either Methylomicrobium buryatense 5 GB1S (5G) or Bacillus methanolicus (BM). Abbreviations are listed in Supplementary Table 4. All data were done with n = 3, biological repeats. Source data are provided as a Source Data file.