Fig. 3: Roles of enzyme abundance and flux in structural evolution.
From: The role of metabolism in shaping enzyme structures over 400 million years
a, Protein abundance was determined using proteomics with data-independent acquisition (Supplementary Methods). b, Mean conservation ratio and the mean log2-transformed protein abundances for 9 of the 27 investigated species measured during exponential growth in minimal medium (n = 491). The orthogroup containing the Thi5/11/12/13p family is highlighted in red, other enzymes of the thiamine biosynthetic pathway are highlighted in purple. The solid line indicates the best linear fit, the dashed line denotes the axis median. c, Spearman’s correlation between protein abundance and conservation ratio for all tested enzymes as well as broken down according to enzyme class (numbers are adjusted according to the presence of protein abundance data). *Padj. < 0.05. d, Correlation between different measures of predicted flux (median, c.v. and number of species (n = 329) with flux through a given orthogroup) and conservation ratio for all tested enzymes, broken down in each column according to the enzyme class. For the flux median and c.v., the Spearman’s correlation was used, and the Kendall τ correlation was used for the number of species. The number in brackets indicates the number of enzymes per class. *Padj. < 0.05. e, Violin plot of the c.v. of the fluxes for the orthogroups in the first and last quartile of conservation ratio (blue) or protein abundance (orange). f, The thiamine biosynthesis pathway is shown. Heat maps underneath enzymes indicate the Z-scores of the mean conservation ratio, mean log2-transformed protein abundance and averaged cost. The Thi5/11/12/13p family and Thi4p undergo suicide reactions in which they lose a histidine and cysteine residue, respectively. Illustrations in a were created using BioRender. Heineike, B. (2025) https://BioRender.com/r831qhq. HMP, 4‐amino‐2‐methyl‐5‐pyrimidine; HMP-P, 4‐amino‐2‐methyl‐5‐pyrimidine phosphate; HMP-PP, 4‐amino‐2‐methyl‐5‐pyrimidine diphosphate; LC–MS, liquid chromatography–mass spectrometry; NAD+, nicotinamide adenine dinucleotide; TDP, thiamine diphosphate; TMP, thiamine phosphate.
