(One-carbon) Metabolism

"There are two kinds of organisms which stand out as the biosynthetic virtuosi of the living world – the autotrophs and the methylotrophs."  J.R. Quayle, 1982

Methylotrophs and autotrophs are both capable of carbon fixation. Methylotrophs generate energy from reduced one-carbon compounds and are able to synthesize all of their cellular constituents from the one-carbon source. In contrast, autotrophs perform their biosynthesis from carbon dioxide and require a separate energy source. The most important reduced one-carbon substrates are methanol and methane, which offer industrial possibilities as renewable feedstocks.

The one-carbon metabolism of bacteria has intrigued our group and others for a long time, and elucidation of the mechanisms enabling growth solely on reduced one-carbon compounds has been a longstanding and challenging goal. Previously, we discovered the pathway and novel enzymes involved in the conversion of the central metabolic intermediate formaldehyde to carbon dioxide and demonstrated that tetrahydromethanopterin as well as methylofuran-dependent enzymes are involved in this process in a large variety of bacterial species. We are using carbon isotope-labeling strategies to uncover routes of one-carbon conversion in methylotrophs and conducted the first identification of the essential genome involved in the model methylotroph. Apart from elucidating the biochemistry of natural methylotrophs, the laboratory uses synthetic biology approaches and generated the first engineered methylotrophic Escherichia coli strain that requires methanol for growth.

The laboratory initiated research on half-lives of essential organic coenzymes in major model microorganisms. We developed long-term dynamic labeling experiments and found that PLP, NAD(P), flavins and coenzyme A are maximally long-lived, are propagated over generations of cells, and are essentially produced to compensate for dilution by growth. Currently, we are investigating coenzyme homeostasis under environmentally challenging conditions.

We operate high-resolution mass spectrometers for metabolomics of free-living and host-associated bacteria and develop novel software tools to facilitate LC-MS data analysis (eMZed, external pageDynaMetexternal page)

Selected publications:

Hemmann JL, Brühwiler MR, Bortfeld-Miller M, Vorholt JA (2021) Structural diversity of the coenzyme methylofuran and identification of enzymes for the biosynthesis of its polyglutamate side chain. J Biol Chem. 296:100682. [external pageAbstract]

Keller P, Noor E, Meyer F, Reiter MA, Anastassov S, Kiefer P, Vorholt JA (2020) Methanol-dependent Escherichia coli strains with a complete ribulose monophosphate cycle. Nat Commun. 11:5403. [external pageAbstract]

Hartl J, Kiefer P, Kaczmarczyk A, Mittelviefhaus M, Meyer F, Vonderach T, Hattendorf B, Jenal U, Vorholt JA (2020) Untargeted metabolomics links glutathione to bacterial cell cycle progression. Nat Metab. 2020 Feb;2(2):153-166. [external pageAbstract]

Erb TJ, Keller P, Vorholt JA (2019) Escherichia coli in Auto(trophic) Mode. Cell. 2019 Nov 27;179(6):1244-1245. [external pageAbstract]

Hemmann JL, Wagner T, Shima S, Vorholt JA (2019) Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites. Proc Natl Acad Sci USA. 51:25583-25590. [external pageAbstract]

Meyer F, Keller P, Hartl J, Gröninger OG, Kiefer P, Vorholt JA (2018) Methanol-essential growth of Escherichia coli. Nat Commun. 9:1508.
[external pageAbstract]

Hartl J, Kiefer P, Meyer F, Vorholt JA (2017) Longevity of coenzymes allows minimal de novo biosynthesis in microorganisms. Nat Microbiol 2:17073. [external pageAbstract]

Ochsner AM, Christen M, Hemmerle L, Peyraud R, Christen B, Vorholt JA (2017) Transposon sequencing uncovers an essential regulatory function of phosphoribulokinase for methylotrophy. Curr. Biol. 27:2579-2588. [external pageAbstract]

Hemmann JL, Saurel O, Ochsner AM, Stodden BK, Kiefer P, Milon A, Vorholt JA (2016) The one-carbon carrier methylofuran from Methylobacterium extorquens AM1 contains a large number of α- and γ-linked glutamic acid residues. J. Biol Chem. 2016 291:9042-51. [external pageAbstract]

Kiefer P, Schmitt U, Müller JE, Hartl J, Meyer F, Ryffel F, Vorholt JA (2015) DynaMet: a fully automated pipeline for dynamic LC-MS data. Anal Chem. 87:9679-86. [external pageAbstract]

Müller JEN, Meyer F, Litsanov B, Kiefer P, Potthoff E, Heux S, Quax WJ, Wendisch VF, Brautaset T, Portais J-C,  Vorholt JA (2015) Engineering Escherichia coli for methanol conversion. Metabol. Eng. 28:190-201 external page[Abstract]  

Martano G, Delmotte N, Kiefer P, Christen P, Kentner D, Bumann D, Vorholt JA (2015) Fast sampling method for mammalian cell metabolomics analyses using liquid chromatography-mass spectrometry. Nature Protocols 10:1-11 external page[Abstract]  

Ochsner AM, Sonntag F, Buchhaupt M, Schrader J, Vorholt JA (2015) Methylobacterium extorquens: methylotrophy and biotechnological applications. Appl Microbiol Biotechnol. 99:517-534 external page[Abstract]  

Müller JEN, Heggeset TM, Wendisch VF, Vorholt JA, Brautaset T (2015) Methylotrophy in the thermophilic Bacillus methanolicus, basic insights and application for commodity production from methanol. Appl. Microbiol. Biotechnol. 99:535-551 external page[Abstract]

Kentner D, Martano G, Callon M, Chiquet P, Brodmann M, Burton O, Wahlander A, Nanni P, Delmotte N, Grossmann J, Limenitakis J, Schlapbach R, Kiefer P, Vorholt JA, Hiller S, Bumann D (2014) Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth. Proc. Natl. Acad. Sci. USA 111:9929-34 external page[Abstract]

Müller JEN, Litsanov B, Bortfeld-Miller M, Trachsel C, Grossmann J, Brautaset T, Vorholt JA (2014) Proteome analysis of the thermophilic methylotroph Bacillus methanolicus MGA3. Proteomics 14:725-737 external page[Abstract]  

Ochsner A, Müller JEN, Mora CA, Vorholt JA (2014) In vitro activation of NAD-dependent alcohol dehydrogenases by Nudix hydrolases is more widespread than assumed. FEBS Letters. 588:2993-2999 external page[Abstract]

Kiefer P, Schmitt U, Vorholt JA (2013) eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows. Bioinformatics 1:963-4 external page[Abstract]

Erb TJ, Kiefer P, Hattendorf B, Günther D, Vorholt JA (2012) GFAJ-1 is an arsenate-resistant, yet phosphate-dependent organism. Science 337:467-470 external page[Abstract]

Schneider K, Peyraud R, Kiefer P, Delmotte N, Portais J.-C., Vorholt JA (2012) The ethylmalonyl-CoA pathway is used in place of the glyoxylate cycle by Methylobacterium extorquens AM1 during growth on acetate. J. Biol. Chem. 287:757-766 external page[Abstract]

Peyraud P, Kiefer P, Christen P, Portais JC, Vorholt JA (2012) Co-consumption of methanol and succinate by Methylobacterium extorquens AM1. PLoS One 7:e48271 external page[Abstract]

Peyraud P, Schneider K, Kiefer P, Massou S, Vorholt JA, Portais J-C (2011) Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1. BMC Systems Biol. 5:189 external page[Abstract]

Kiefer P, Delmotte N, Vorholt JA (2011) Nanoscale ion-pair reversed-phase HPLC-MS for sensitive metabolome analysis. Anal. Chem. 83:850-855 external page[Abstract]

Peyraud R, Kiefer P, Christen P, Massou S, Portais JC, Vorholt JA (2009) Demonstration of the ethylmalonyl-CoA pathway using 13C metabolomics. Proc. Natl. Acad. Sci USA 106:4846-4851 external page[Abstract]

Schrader J, Schilling M, Holtmann D, Sell D, Villela Filho M, Marx A, Vorholt JA (2009) Methanol based industrial biotechnology: current status and future perspectives of methylotrophic bacteria. Trends Biotechnol. 27:106-115 external page[Abstract]

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