a Volcano plot of differential transcript levels as determined by RNA sequencing (n = 3). b Gene transcript level changes related to central metabolism pathways and oxidative phosphorylation between MX-14 cultivated with 15 g/L vs. 4 g/L methanol. Significant differentially expressed genes were defined as having a false discovery rate (FDR) < 0.05 and a log2(Fold change) >0.5 or <−0.5. Up-regulated and down-regulated enzymes are indicated with red and blue, respectively. Enzymes: alcohol dehydrogenase (AdhA), xylulokinase (XylB), 6-phosphofructokinase (PfkA), fructose bisphosphate aldolase (Fba), triosephosphate isomerase (Tpi), glyceraldehyde-3-phosphate dehydrogenase (Gap), phosphoglycerate kinase (Pgk), phosphoglycerate mutase (GpmA), enolase (Eno), pyruvate kinase (Pyk), FMN-dependent l-lactate dehydrogenase (LldA), NAD-dependent l-lactate dehydrogenase (Ldh), FAD/FMN-containing d-lactate dehydrogenase (Dld), pyruvate dehydrogenase (Pdh), acetyl-CoA hydrolase (ActA), phosphotransacetylase (Pta), phosphoenolpyruvate carboxykinase (Pck), phosphoenolpyruvate carboxylase (Ppc), citrate synthase (GltA), aconitate hydratase (Acn), isocitrate dehydrogenase (Icd), α-oxoglutarate dehydrogenases E1 component (OdhA), dihydrolipoamide acyltransferases (SucB), dihydrolipoamide dehydrogenase (Lpd), succinyl-CoA synthetase (SucCD), succinate dehydrogenase (SdhCAB), fumarate hydratase (FumC), malate dehydrogenase (Madh), isocitrate lyase (Icl), malate synthase (AceB), 3-deoxy-7-phosphoheptulonate synthase (AroF), aspartokinase (LysC), aspartate-semialdehyde dehydrogenase (Asd), homoserine kinase (ThrB), O-acetyl-l-homoserine sulfhydrylase (MetY), methionine synthase I (MetH), methionine synthase II (MetE), threonine dehydratase (IlvA), acetolactate synthase (IlvBN), ketol-acid reductoisomerase (IlvC), dihydroxyacid dehydratase (IlvD), branched-chain amino acid aminotransferase (IlvE), isopropylmalate synthase (LeuA), FAD-containing NADH dehydrogenase (Ndh), cytochrome bc1c complex (QcrCAB), cytochrome aa3 complex (CtaCDEF), ATP synthase (α, Cgl1210; β, Cgl1212; γ, Cgl1211, δ, Cgl1209; ε, Cgl1213; a, Cgl1206; b, Cgl1208; c, Cgl1207). Metabolites: fructose-1,6-bisphosphate (F16dP), dihydroxyacetone phosphate (DHAP), 3-deoxy-arabino-heptulonate 7-phosphate (DAHP), menaquinone (MQ), and menaquinol (MQH2).