Biology subjects

Stulke, J.

Publications and source records attributed to Stulke, J..

4 recordsLinked to original sources

bioRxiv2024

A new framework for SubtiWiki, the database for the model organism Bacillus subtilis

Bacillus subtilis is a Gram-positive model bacterium and one of the most-studied and best understood organisms. The complex information resulting from its investigation is compiled in the database SubtiWiki (https://subtiwiki.uni-goettingen.de/v5) in an integrated and intuitive manner. To enhance the utility of SubtiWiki, we have added novel features such as a viewer to interrogate conserved genomic organization, a widget that shows mutant fitness data for all non-essential genes, and a widget showing protein structures, structure predictions and complex structures. Moreover, we have integrated metabolites as new entities. The new framework also includes a documented API, enabling programmatic access to data for computational tasks. Here we present the recent developments of SubtiWiki and the current state of the data for this organism. Key pointsO_LISubtiWiki is the most popular database for the model bacterium Bacillus subtilis. C_LIO_LITo facilitate the development of new research hypotheses, SubtiWiki has been enhanced by graphical information on conserved genomic organization, mutant fitness data, and a new protein structure viewer. C_LIO_LIMetabolites have been integrated as entities on their own with dedicated pages, interactive information on reactions and metabolite functions as well as their interactions. C_LI

bioinformatics↗

bioRxiv2024

Coenzyme A biosynthesis in Bacillus subtilis: Discovery of a novel precursor metabolite for salvage and its uptake system

The Gram-positive model bacterium Bacillus subtilis is used for many biotechnological applications, including the large-scale production of vitamins. For vitamin B5, a precursor for coenzyme A synthesis, there is so far no established fermentation process available, partly due to the incomplete knowledge on the metabolic pathways that involve this vitamin. In this study, we have elucidated the complete pathways for the biosynthesis pantothenate and coenzyme A in B. subtilis. We have identified the enzymes involved in the pathway and have identified a salvage pathway for coenzyme A acquisition that acts on complex medium even in the absence of pantothenate synthesis. This pathway requires rewiring of sulfur metabolism resulting in the expression of a cysteine transporter. In the salvage pathway, the bacteria import cysteinopantetheine, a novel naturally occurring metabolite, using the cystine transport system TcyJKLMN. This work lays the foundation for the development of effective processes for vitamin B5 production.

microbiology↗

bioRxiv2024

RfaA (YqhY), a novel adaptor protein, controls metabolite-sensitive protein degradation in Bacillus subtilis

The carboxylation of acetyl-CoA is the committed step of fatty acid synthesis catalyzed by the multisubunit acetyl-CoA carboxylase (ACCase). However, the mechanisms that control the activity of this enzyme are poorly understood. Here, we identify the so far unknown protein RfaA (YqhY) of the model bacterium Bacillus subtilis as a regulator of fatty acid acquisition that targets the AccC subunit of ACCase for degradation. RfaA interacts with both AccC and the ClpE unfoldase subunit of the ClpEP protease complex. While the former interaction is not sensitive to the physiological conditions, RfaA interacts with ClpE only in the absence of the global amino group donor glutamate. This results in the degradation of AccC in the absence of glutamate. The inactivation of the rfaA gene results in the accumulation of fatty acids in the cell and in the formation of lipid droplets which are toxic for the bacteria. The reduced fatty acid synthesis in the absence of glutamate as a result of RfaA-and ClpEP-dependent degradation of AccC thus prevents intoxication of the cells by fatty acids. Our findings suggest that the degradation of enzymes that catalyze the committed step of biosynthetic pathways might be an important mechanism to control cellular homeostasis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/580884v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1f09555org.highwire.dtl.DTLVardef@1dc12e8org.highwire.dtl.DTLVardef@15d6961org.highwire.dtl.DTLVardef@1b1923e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

How to deal with toxic amino acids: the bipartite AzlCD complex exports histidine in Bacillus subtilis

In the Gram-positive model bacterium Bacillus subtilis, the presence of the amino acid glutamate triggers potassium uptake due to the glutamate-mediated activation of the potassium channel KtrCD. As a result, the intracellular accumulation of glutamate is toxic in strains lacking the second messenger cyclic di-AMP since these cells are unable to limit potassium uptake. We observed that the presence of histidine, which is degraded to glutamate, is also toxic for a B. subtilis strain that lacks all three c-di-AMP synthesizing enzymes. However, suppressor mutants emerged, and whole genome sequencing revealed mutations in the azlB gene encoding the repressor of the azl operon. This operon encodes an exporter and an importer for branched-chain amino acids. The suppressor mutations result in overexpression of the azl operon. Deletion of the azlCD genes encoding the branched-chain amino acid exporter restored the toxicity of histidine indicating that this exporter is required for histidine export and resistance to otherwise toxic levels of the amino acid. The higher abundance of the amino acid exporter AzlCD increased the extracellular concentration of histidine, thus confirming the new function of AzlCD as a histidine exporter. Unexpectedly, AzlB-mediated repression of the operon remains active even in the presence of amino acids suggesting that expression of the azl operon requires mutational inactivation of AzlB. IMPORTANCEAmino acids are building blocks for protein biosynthesis in each living cell. However, due to their reactivity as well as the similarity between several amino amino acids, they may also be involved in harmful reactions or in non-cognate interactions and thus be toxic. Bacillus subtilis can deal with otherwise toxic histidine by overexpressing a bipartite amino acid exporter AzlCD. Although encoded in an operon that also contains a gene for an amino acid importer, the corresponding genes are not expressed, irrespective of the availability or not of amino acids in the medium. This suggests that the azl operon is a last resort to deal with histidine stress that can be expressed due to mutational inactivation of the cognate repressor, AzlB.

microbiology↗