Figure 1.
Frequency of anaerobic (in blue) and aerobic (in red) enzymes in six categories (EC1∼EC6).
Table 1.
Cofactor usage in anaerobic and aerobic oxidoreductases.
Figure 2.
Most prevalent scaffolds of aerobic metabolism.
The occurrence number of the scaffold in aerobic metabolite space is labeled at the top left of the structure.
Figure 3.
Structural cluster map of anaerobic and aerobic metabolites (represented with blue dots and red dots, respectively).
In this map, the distance of two compounds is determined by their Tanimoto similarity (based on shared substructural fragments). Similar compounds are pooled together into clusters. The dot size indicates the number of the clustered compounds (with Tanimoto similarity >0.85). The largest dots represent clusters containing more than 10 similar compounds. Some representative compounds for the major clusters are presented around the map.
Table 2.
Median/mean values of chemical property descriptors for anaerobic and aerobic metabolites.
Figure 4.
Chemical space of anaerobic and aerobic metabolites defined by the first two factors from an analysis of 20 descriptors.
Aerobic metabolites (in blue) preferentially occupy the left and upper parts of the space, while anaerobic metabolites (in red) concentrate in the relatively lower part. Oxygen appears to have greatly helped metabolism to explore a wider chemical space.
Figure 5.
Amino acid compositions of catalytic sites in anaerobic (in blue) and aerobic (in red) enzymes.
It can be seen that anaerobic enzymes use polar amino acid residues (e.g., Asp, Glu, Lys and Arg) in catalytic sites more frequently (P<0.05), while aerobic enzymes use non-polar residues (e.g., Trp and Ile) more often (P<0.05).
Figure 6.
Chemical space of anaerobic metabolites defined by the first two factors from an analysis of 20 descriptors, showing early anaerobic metabolites (in magenta) preferentially occupying the right and lower parts of the space.
Table 3.
Averaged net changes (from reactants to products) of some properties associated with polarity for anaerobic and aerobic reaction pairs.
Figure 7.
Polarity variation trends in pathways for biosynthesis of steroids and diterpenoids.
Each metabolite is represented with a dot. Blue lines connect anaerobic metabolites (left) and red lines connect aerobic metabolites (right). The metabolite polarity descriptor (AlogP98) is indicated by different colors, from blue (strong polar) to red (strong non-polar). The polarity of metabolites decreases steadily to the minimum with the progression of anaerobic reactions (from left to right). In contrast, the polarity of aerobic metabolites increases with the expansion of aerobic networks but is on average still weaker than that of anaerobic metabolites.