Amino acid metabolism

Amino acids are the building blocks of all proteins and can either be synthesized or taken up from the environment. Alternatively, proteins can be degraded and the released peptides and amino acids can be utilized. Glutamate occupies a special position among the 22 proteinogenic amino acids because it is the major cellular amino group donor that is required for the biosynthesis of nitrogen-containing molecules (Figure A). Besides its role as an amino group donor, glutamate has many other important functions in the cell. Therefore, it is not surprising that glutamate is the dominating intracellular metabolite. In the Gram-positive model bacterium Bacillus subtilis, glutamate is synthesized from ammonium and 2-oxoglutarate by the combined action of the glutamine synthetase (GS) and the glutamate synthase (GOGAT) (Figure B). B. subtilis also possesses glutamate dehydrogenases (GDHs). However, the GDHs are strictly devoted to glutamate degradation in vivo. Interestingly, the GS, GOGAT and the GDHs belong to the class of moonlighting proteins, as the enzymes possess additional functions alongside their role in metabolism (http://www.moonlightingproteins.org). While the GS and GDHs are trigger enzymes that control gene expression through the interaction with DNA-binding transcription factors, the glutamate-synthesizing GOGAT acts as a counter enzyme, inactivating a GDH to prevent a futile cycle (Figure B). 

 

Why are we interested in amino acid metabolism in B. subtilis?

  • Genetic data indicate that the GDHs convert a DNA-binding activator protein into a repressor protein.
  • Canonical metabolic pathways for glutamate biosynthesis and degradation can be bypassed by a few mutations. 
  • B. subtilis is a very well-studied bacterium. However, not all of the transporters for amino acid uptake are known.

 

Publications 

Gibhardt J, Lieber MM, Götz CS, Völker F, Blank LM, Forchhammer K, Jayaraman V, Noda-Garcia L, Commichau FM (2026) Moonlighting in metabolism: bifunctional enzymes control nitrogen metabolism in Bacillus subtilis. Microbiol Mol Biol Rev. 13: e0043025. 

Völker F, Maaß S, Phan ANT, Gibhardt J, Commichau FM Blank LM (2025) High glutamate demand enables simultaneous consumption of glycerol and citrate despite carbon catabolite repression in engineered Bacillus subtilis strains. Metab Eng. 91: 379-388.

Mardoukhi MSY, Rapp J, Irisarri I, Gunka K, Link H, Marienhagen J, de Vries J, Stülke J, Commichau FM (2024) Metabolic rewiring enables ammonium assimilation via a non-canonical fumarate-based pathway. Microb Biotechnol. 17: e14429.

Meißner J, Königshof M, Wrede K, Warneke R, Mardoukhi MSY, Commichau FM, Stülke J (2024) Control of asparagine homeostasis in Bacillus subtilis: identification of promiscuous amino acid importers and exporters. J Bacteriol. 206: e00420-23.

Dormeyer M, Lentes S, Richts B, Heermann R, Ischebeck T, Commichau FM (2019) Variants of the Bacillus subtilis LysR-type regulator GltC with altered activator and repressor function. Front Microbiol. 10: 2321.

Reuß DR, Rath H, Thürmer A, Benda M, Daniel R, Völker U, Mäder U, Commichau FM, Stülke J (2018) Changes in DNA topology affect the global transcription landscape and allow rapid growth of a Bacillus subtilis strain lacking carbon catabolite repression. Metab Eng 45: 171-179.

Dormeyer M, Lübke AL, Müller P, Lentes S, Reuß DR, Thürmer A, Stülke J, Daniel R, Brantl S, Commichau FM (2017) Hierarchical mutational events compensate for glutamate auxotrophy of a Bacillus subtilis gltC mutant. Environ Microbiol Rep. 9: 279-289.

Stannek L, Thiele MJ, Ischebeck T, Gunka K, Hammer E, Völker U, Commichau, FM (2015) Evidence for synergistic control of glutamate biosynthesis by glutamate dehydrogenases and glutamate in Bacillus subtilis. Environ Microbiol. 17: 3379-3390.

Stannek L, Gunka K, Care RA, Gerth U, Commichau FM (2015) Factors that mediate and prevent degradation of the inactive and unstable GudB protein in Bacillus subtilis. Front Microbiol. 7: 758.

Stannek L, Egelkamp R, Gunka K, Commichau FM (2014) Monitoring intraspecies competition in a bacterial cell population by co-cultivation of fluorescently labelled strains. J Vis Exp 18: e51196.

Gunka J, Stannek L, Care RA, Commichau FM (2013) Selection-driven accumulation of suppressor mutants in Bacillus subtilis: the apparent high mutation frequency and the rapid clonal expansion of gudB(+)suppressors are due to growth under selection. PLoS One 8: e66120.

Gunka K, Commichau FM (2012) Control of glutamate metabolism in Bacillus subtilis: A complex interplay between ammonium assimilation, glutamate biosynthesis and degradation. Mol Microbiol. 85: 213-224.

Gunka K, Gerwig J, Tholen S, Herzberg C, Stülke J, Commichau FM (2012) A high frequency mutation in Bacillus subtilis: decryptification of the gudB glutamate dehydrogenase gene. J Bacteriol 194: 1036-1044.

Gunka K, Newman J, Commichau FM, Herzberg C, Rodrigues C, Hewitt L, Lewis R, Stülke J (2010) Functional dissection of a trigger enzyme: Mutations of the Bacillus subtilis glutamate dehydrogenase RocG that affect differentially its catalytic activity and regulatory properties. J Mol Biol. 400: 815-827.

Commichau FM, Stülke J (2008) Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression. Mol Microbiol. 67: 692-702.

Herzberg C, Flórez Weidinger LA, Dörrbecker B, Hübner S, Stülke J, Commichau FM (2007) SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo. Proteomics 12: 4032-4035.

Commichau FM, Herzberg C, Valerius O, Tripal P, Stülke J (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in Bacillus subtilis: The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol. 65: 642-654.

Commichau FM, Wacker I, Schleider J, Blencke HM, Reif I, Tripel I, Stülke J (2007) Characterization of Bacillus subtilis mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113.

Commichau FM, Forchhammer K, Stülke J (2006) Regulatory links between carbon and nitrogen metabolism. Curr Opin Microbiol. 9: 167-172.