Supplementary experimental procedures.

Fig. S1. Phylogenetic profiling of 6-phosphofructokinases in bacteria. Phylogenetic profiling reveals that many genomes of γ-proteobacteria, firmicutes, bacteroidetes, Acidobacterium and some cyanobacteria contain either a pfkA or pfkB gene, while it is absent in most α-proteobacteria, β-proteobacteria and Chlamydiae genomes. Furthermore, phylogenetic profiling indicates that pfk genes are usually absent in the genomes of most aerobic microorganisms (e.g. Pseudomonas species), while most anaerobic or facultative anaerobic organisms contain a pfkA gene. Since little energy is generated from C substrates in strict anaerobic species, the relative gain in ATP yield increases significantly when 6-phosphofructokinase (i.e. a complete Embden–Meyerhof–Parnas glycolytic pathway) is present.

Fig. S2. Scheme of the pathways involved in glucose catabolism in Pseudomonas putida KT2440. After the initial phosphorylation of glucose, catalysed by glucokinase (Glk), the resulting glucose-6-P is channelled through the Entner–Doudoroff pathway (Edd/Eda) via its conversion into 6-P-gluconate and 6-P-2-keto-3-deoxygluconate to finally yield pyruvate and glyceraldehyde-3-P. Glucose can also be converted into gluconate, 2-ketogluconate and 6-P-2-ketogluconate in the so-called gluconate and 2-ketogluconate loops but these intermediates are ultimately converted into 6-P-gluconate and yield the same C3 compounds as mentioned above. Pyruvate is transformed into acetyl-coenzyme A (CoA) through the activity of the pyruvate dehydrogenase complex (AceEF and other components, as depicted) in a NAD+-dependent reaction. Although acetyl-CoA can meet different fates depending on further catabolic steps, it is mainly oxidized in the tricarboxylic acid cycle. The reducing equivalents therein produced as NADH are used as electron donors in the respiratory chain, thereby generating ATP during the oxidative phosphorylation process. The relevant enzymatic steps are identified in parentheses by means of their locus (PP) numbers as annotated by Nelson and colleagues (2002). P, inorganic phosphate; PQQ, pyrroloquinoline quinone.

Fig. S3. Sensitivity of E. coli MG1655, A. tumefaciens C58C1, P. putida KT2440 and P. aeruginosa PAO1 to oxidative stress imposed by diamide. The resistance to diamide depends on NADPH-dependent thioredoxins, so that the response of the bacteria to the stress generated by this compound ultimately depends on the intracellular redox state. As it can be seen in the inhibition halos for each species, P. putida and P. aeruginosa present a higher tolerance to diamide than E. coli and A. tumefaciens.

Table S1. Bacterial strains and plasmids used in this work.

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