Continuous Culture Adaptation of Methylobacterium extorquens AM1 and TK 0001 to Very High Methanol Concentrations

Sophia Belkhelfa (1) , David Roche (2) , Ivan Dubois (1) , Anne Berger (1) , Valérie A Delmas (1) , Laurence Cattolico (1) , Alain Perret (1) , Karine Labadie (3) , Aude C Perdereau (3) , Ekaterina Darii (1) , Emilie Pateau (1) , Véronique de Berardinis (1) , Marcel Salanoubat (1) , Madeleine Bouzon (1) , Volker Doring (1)

1 UMR 8030 - Génomique métabolique
2 LABGeM - Analyse Bio-Informatique pour la Génomique et le Métabolisme
3 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]

The bio-economy relies on microbial strains optimized for efficient large scale production of chemicals and fuels from inexpensive and renewable feedstocks under industrial conditions. The reduced one carbon compound methanol, whose production does not involve carbohydrates needed for the feed and food sector, can be used as sole carbon and energy source by methylotrophic bacteria like Methylobacterium extorquens AM1. This strain has already been engineered to produce various commodity and high value chemicals from methanol. The toxic effect of methanol limits its concentration as feedstock to 1% v/v. We obtained M. extorquens chassis strains tolerant to high methanol via adaptive directed evolution using the GM3 technology of automated continuous culture. Turbidostat and conditional medium swap regimes were employed for the parallel evolution of the recently characterized strain TK 0001 and the reference strain AM1 and enabled the isolation of derivatives of both strains capable of stable growth with 10% methanol. The isolates produced more biomass at 1% methanol than the ancestor strains. Genome sequencing identified the gene metY coding for an O-acetyl-L-homoserine sulfhydrylase as common target of mutation. We showed that the wildtype enzyme uses methanol as substrate at elevated concentrations. This side reaction produces methoxine, a toxic homolog of methionine incorporated in polypeptides during translation. All mutated metY alleles isolated from the evolved populations coded for inactive enzymes, designating O-acetyl-L-homoserine sulfhydrylase as a major vector of methanol toxicity. A whole cell transcriptomic analysis revealed that genes coding for chaperones and proteases were upregulated in the evolved cells as compared with the wildtype, suggesting that the cells had to cope with aberrant proteins formed during the adaptation to increasing methanol exposure. In addition, the expression of ribosomal proteins and enzymes related to energy production from methanol like formate dehydrogenases and ATP synthases was boosted in the evolved cells upon a short-term methanol stress. D-lactate production Frontiers in Microbiology | www.frontiersin.org 1

Mots clés: methylotrophic bacteria; directed evolution; continuous culture; genomics; transcriptomics; lactate

Domaines: Sciences du Vivant [q-bio]; Biochimie, Biologie Moléculaire

Sophia Belkhelfa, David Roche, Ivan Dubois, Anne Berger, Valérie A Delmas, et al.. Continuous Culture Adaptation of Methylobacterium extorquens AM1 and TK 0001 to Very High Methanol Concentrations. Frontiers in Microbiology, 2019, 10, ⟨10.3389/fmicb.2019.01313⟩. ⟨hal-02323743⟩