Ornithine is the central intermediate in the arginine degradative pathway and its regulation in Bacillus subtilis

Warneke, Robert; Garbers, Tim Benedict; Herzberg, Christina; Aschenbrandt, Georg; Ficner, Ralf; Stülke, Jörg

doi:10.1016/j.jbc.2023.104944

Cited by 9 publications

(9 citation statements)

References 39 publications

(66 reference statements)

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“…The formation of OLs induced the expression of genes related to the arginine synthesis (Fig 3c, perturbations C, D, and E). Because ornithine is an intermediate of arginine synthesis in E. coli and is also used as a precursor for OL synthesis (Warneke et al 2023), we hypothesize that the expression of OlsFC may cause arginine limitation. This perceived low concentration of intracellular arginine could explain the induction of arginine synthesis genes in the presence of OLs.…”

Section: Discussionmentioning

confidence: 99%

EnhancingEscherichia coliAbiotic Stress Resistance through Ornithine Lipid Formation

Bedoya-Pérez

Aguilar-Vera

Utrilla

et al. 2023

Preprint

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Escherichia coli is a common host for biotechnology and synthetic biology applications. During growth and fermentation, the microbes are often exposed to stress conditions, like variations in pH or solvent concentrations and it has been described that bacterial membranes play a key role in response to abiotic stresses. Ornithine lipids (OLs) are a group of membrane lipids whose presence and synthesis have been related to stress resistance in different bacteria. In this study, we engineered different E. coli strains to produce unmodified OLs and hydroxylated OLs by expressing the synthetic operon olsFC. Our results showed that OL formation improved pH resistance and increased biomass under phosphate limitation. Transcriptome analysis revealed that OL-forming strains differentially expressed stress and membrane-related genes. OL-producing strains also showed better growth in the presence of the ionophore carbonyl cyanide 3-chlorophenylhydrazone (CCCP), suggesting reduced proton leakiness. Furthermore, our engineered strains showed improved heterologous violacein production at phosphate limitation and low pH. Overall, this study demonstrates the potential of engineering the E. coli membrane composition for constructing robust hosts for biotechnology and synthetic biology applications.

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Section: Discussionmentioning

confidence: 99%

EnhancingEscherichia coliAbiotic Stress Resistance through Ornithine Lipid Formation

Bedoya-Pérez

Aguilar-Vera

Utrilla

et al. 2023

Preprint

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“…β-alanine, the only naturally occurring β-amino acid, is required as a precursor for the biosynthesis of coenzyme A ( 2 , 3 ). Citrulline, ornithine, and γ-aminobutyrate can be used as carbon and nitrogen sources, and the latter two also serve as inducers for transcription factors in Bacillus subtilis ( 4 – 6 ). Finally, citrulline serves as a compatible solute to protect the cell from osmotic stress ( 7 ).…”

Section: Introductionmentioning

confidence: 99%

Control of three-carbon amino acid homeostasis by promiscuous importers and exporters in Bacillus subtilis : role of the “sleeping beauty” amino acid exporters

Warneke,

Herzberg,

Daniel

et al. 2024

mBio

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The Gram-positive model bacterium Bacillus subtilis can acquire amino acids by import, de novo biosynthesis, or degradation of proteins and peptides. The accumulation of several amino acids inhibits the growth of B. subtilis , probably due to misincorporation into cellular macromolecules such as proteins or peptidoglycan or due to interference with other amino acid biosynthetic pathways. Here, we studied the adaptation of B. subtilis to toxic concentrations of the three-carbon amino acids L-alanine, β-alanine, and 2,3-diaminopropionic acid, as well as the two-carbon amino acid glycine. Resistance to the non-proteinogenic amino acid β-alanine, which is a precursor for coenzyme A biosynthesis, is achieved by mutations that either activate a cryptic amino acid exporter, AexA (previously YdeD), or inactivate the amino acid importers AimA, AimB (previously YbxG), and BcaP. The aexA gene is very poorly expressed under most conditions studied. However, mutations affecting the transcription factor AerA (previously YdeC) can result in strong constitutive aexA expression. AexA is the first characterized member of a group of amino acid exporters in B. subtilis , which are all very poorly expressed. Therefore, we suggest to call this group “sleeping beauty amino acid exporters.” 2,3-Diaminopropionic acid can also be exported by AexA, and this amino acid also seems to be a natural substrate of AerA/AexA, as it can cause a slight but significant induction of aexA expression, and AexA also provides some natural resistance toward 2,3-diaminopropionic acid. Moreover, our work shows how low-specificity amino acid transporters contribute to amino acid homeostasis in B. subtilis . IMPORTANCE Even though Bacillus subtilis is one of the most-studied bacteria, amino acid homeostasis in this organism is not fully understood. We have identified import and export systems for the C2 and C3 amino acids. Our work demonstrates that the responsible amino acid permeases contribute in a rather promiscuitive way to amino acid uptake. In addition, we have discovered AexA, the first member of a group of very poorly expressed amino acid exporters in B. subtilis that we call “sleeping beauty amino acid exporters.” The expression of these transporters is typically triggered by mutations in corresponding regulator genes that are acquired upon exposure to toxic amino acids. These exporters are ubiquitous in all domains of life. It is tempting to speculate that many of them are not expressed until the cells experience selective pressure by toxic compounds, and they protect the cells from rare but potentially dangerous encounters with such compounds.

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“…This regulatory system allows B. subtilis to grow under fluctuating glutamate concentrations [Jayaraman et al, 2022]. In the presence of arginine, which is converted via ornithine to glutamate, the DNA binding transcription factors AhrC and RocR, of which the latter is triggered by ornithine, activate the transcription of the rocG gene and the encoded GDH RocG [Calogero et al, 1994; Gardan et al, 1995; 1997; Miller et al, 1997; Warneke et al, 2023]. Like the GDH GudB, RocG can also inactivate the GltC protein [Commichau et al, 2007a, 2007b; Stannek et al, 2015].…”

Section: Introductionmentioning

confidence: 99%

Metabolic rewiring compensates for the loss of glutamate and aspartate biosynthesis inBacillus subtilis

Mardoukhi,

Rapp,

Irisarri

et al. 2023

Preprint

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SummaryGlutamate serves as the major cellular amino group donor. InBacillus subtilis, glutamate is synthesized by the combined action of the glutamine synthetase and the glutamate synthase (GOGAT). The glutamate dehydrogenases are devoted to glutamate degradationin vivo. To keep the cellular glutamate concentration high, the genes and the encoded enzymes involved in glutamate biosynthesis and degradation need to be tightly regulated depending on the available carbon and nitrogen sources. Serendipitously, we found that the inactivation of theansRandcitGgenes encoding the repressor of theansABgenes and the fumarase, respectively, enables the GOGAT-deficientB. subtilismutant to synthesize glutamate via a non-canonical fumarate-based ammonium assimilation pathway. We also show that the de-repression of theansABgenes is sufficient to restore aspartate prototrophy of anaspBaspartate transaminase mutant. Moreover, with excess nitrogen,B. subtilismutants lacking fumarase activity show a growth defect that can be relieved byaspBoverexpression, by reducing arginine uptake and by decreasing the metabolic flux through the TCA cycle. It will be interesting to investigate whether theB. subtilisstrain using the alternative glutamate biosynthesis route can evolve in such a way that it robustly grows during nitrogen limitation and excess.

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Ornithine is the central intermediate in the arginine degradative pathway and its regulation in Bacillus subtilis

Cited by 9 publications

References 39 publications

EnhancingEscherichia coliAbiotic Stress Resistance through Ornithine Lipid Formation

EnhancingEscherichia coliAbiotic Stress Resistance through Ornithine Lipid Formation

Control of three-carbon amino acid homeostasis by promiscuous importers and exporters in Bacillus subtilis : role of the “sleeping beauty” amino acid exporters

Metabolic rewiring compensates for the loss of glutamate and aspartate biosynthesis inBacillus subtilis

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