Transcriptional and metabolic adaptations of the methanotroph Methylomicrobium alcaliphilum to high salinity conditions

Methylomicrobium alcaliphilum is an alkaliphilic and halotolerant methanotroph with potential industrial applications as an ectoine producer or as a platform for metabolic engineering. The physiological, transcriptional and metabolic responses of M. alcaliphilum to high NaCl concentrations, have been studied using RNA-seq, metabolic modeling and enzyme activity tests. M. alcaliphilum was revealed to have an unusual respiratory chain, in which complex I is replaced by a Na+ extruding NQR complex (highly upregulated under high salinity conditions) and a Na+ driven ATP synthase that coexists with a more usual H+ driven ATP synthase. A thermodynamic and metabolic model showing the interplay between these different components is presented. Ectoine is the main osmoprotector used by the cells (but its effect is not enough to avoid molecular crowding as a result of large water outflow and the expression of chaperones is necessary). Ectoine synthesis is activated by the transcription of an ect operon that contains 5 genes, including the ectoine hydroxylase coding ectD gene. Enzymatic tests revealed that the product of ectD does not have catalytic activity. A new Genome Scale Metabolic Model for M. alcalyphilum was reconstructed and used to integrate RNA-seq data and reveal a higher flux in the oxidative branch of the penthose phosphate pathway leading to NADPH production and contributing to resistance to oxidative stress.