Commichau, Fabian M.

[["dc.bibliographiccitation.firstpage","1036"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Journal of Bacteriology"],["dc.bibliographiccitation.lastpage","1044"],["dc.bibliographiccitation.volume","194"],["dc.contributor.author","Gunka, Katrin"],["dc.contributor.author","Tholen, Stefan"],["dc.contributor.author","Gerwig, Jan"],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Stuelke, Joerg"],["dc.contributor.author","Commichau, Fabian M."],["dc.date.accessioned","2018-11-07T09:13:08Z"],["dc.date.available","2018-11-07T09:13:08Z"],["dc.date.issued","2012"],["dc.description.abstract","Common laboratory strains of Bacillus subtilis encode two glutamate dehydrogenases: the enzymatically active protein RocG and the cryptic enzyme GudB that is inactive due to a duplication of three amino acids in its active center. The inactivation of the rocG gene results in poor growth of the bacteria on complex media due to the accumulation of toxic intermediates. Therefore, rocG mutants readily acquire suppressor mutations that decryptify the gudB gene. This decryptification occurs by a precise deletion of one part of the 9-bp direct repeat that causes the amino acid duplication. This mutation occurs at the extremely high frequency of 10(-4). Mutations affecting the integrity of the direct repeat result in a strong reduction of the mutation frequency; however, the actual sequence of the repeat is not essential. The mutation frequency of gudB was not affected by the position of the gene on the chromosome. When the direct repeat was placed in the completely different context of an artificial promoter, the precise deletion of one part of the repeat was also observed, but the mutation frequency was reduced by 3 orders of magnitude. Thus, transcription of the gudB gene seems to be essential for the high frequency of the appearance of the gudB1 mutation. This idea is supported by the finding that the transcription-repair coupling factor Mfd is required for the decryptification of gudB. The Mfd-mediated coupling of transcription to mutagenesis might be a built-in precaution that facilitates the accumulation of mutations preferentially in transcribed genes."],["dc.identifier.doi","10.1128/JB.06470-11"],["dc.identifier.isi","000300530800015"],["dc.identifier.pmid","22178973"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/27106"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Amer Soc Microbiology"],["dc.relation.issn","0021-9193"],["dc.title","A High-Frequency Mutation in Bacillus subtilis: Requirements for the Decryptification of the gudB Glutamate Dehydrogenase Gene"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","136"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Archives of Microbiology"],["dc.bibliographiccitation.lastpage","146"],["dc.bibliographiccitation.volume","185"],["dc.contributor.author","Blencke, Hans-Matti"],["dc.contributor.author","Reif, I."],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Detsch, C."],["dc.contributor.author","Wacker, I."],["dc.contributor.author","Ludwig, H."],["dc.contributor.author","Stulke, J."],["dc.date.accessioned","2018-11-07T10:09:35Z"],["dc.date.available","2018-11-07T10:09:35Z"],["dc.date.issued","2006"],["dc.description.abstract","The tricarboxylic acid (TCA) cycle is one of the major routes of carbon catabolism in Bacillus subtilis. The syntheses of the enzymes performing the initial reactions of the cycle, citrate synthase, and aconitase, are synergistically repressed by rapidly metabolizable carbon sources and glutamine. This regulation involves the general transcription factor CcpA and the specific repressor CcpC. In this study, we analyzed the expression and intracellular localization of CcpC. The synthesis of citrate, the effector of CcpC, requires acetyl-CoA. This metabolite is located at a branching point in metabolism. It can be converted to acetate in overflow metabolism or to citrate. Manipulations of the fate of acetyl-CoA revealed that efficient citrate synthesis is required for the expression of the citB gene encoding aconitase and that control of the two pathways utilizing acetyl-CoA converges in the control of citrate synthesis for the induction of the TCA cycle. The citrate pool seems also to be controlled by arginine catabolism. The presence of arginine results in a severe CcpC-dependent repression of citB. In addition to regulators involved in sensing the carbon status of the cell, the pleiotropic nitrogen-related transcription factor, TnrA, activates citB transcription in the absence of glutamine."],["dc.identifier.doi","10.1007/s00203-005-0078-0"],["dc.identifier.isi","000235245800007"],["dc.identifier.pmid","16395550"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/39680"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","0302-8933"],["dc.title","Regulation of citB expression in Bacillus subtilis: integration of multiple metabolic signals in the citrate pool and by the general nitrogen regulatory system"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","18"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Metabolic Engineering"],["dc.bibliographiccitation.lastpage","27"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Meyer, Frederik M."],["dc.contributor.author","Gerwig, Jan"],["dc.contributor.author","Hammer, Elke"],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Voelker, Uwe"],["dc.contributor.author","Stuelke, Joerg"],["dc.date.accessioned","2018-11-07T09:01:42Z"],["dc.date.available","2018-11-07T09:01:42Z"],["dc.date.issued","2011"],["dc.description.abstract","The majority of all proteins of a living cell is active in complexes rather than in an isolated way. These protein-protein interactions are of high relevance for many biological functions. In addition to many well established protein complexes an increasing number of protein-protein interactions, which form rather transient complexes has recently been discovered. The formation of such complexes seems to be a common feature especially for metabolic pathways. In the Gram-positive model organism Bacillus subtilis, we identified a protein complex of three citric acid cycle enzymes. This complex consists of the citrate synthase, the isocitrate dehydrogenase, and the malate dehydrogenase. Moreover, fumarase and aconitase interact with malate dehydrogenase and with each other. These five enzymes catalyze sequential reaction of the TCA cycle. Thus, this interaction might be important for a direct transfer of intermediates of the TCA cycle and thus for elevated metabolic fluxes via substrate channeling. In addition, we discovered a link between the TCA cycle and gluconeogenesis through a flexible interaction of two proteins: the association between the malate dehydrogenase and phosphoenolpyruvate carboxykinase is directly controlled by the metabolic flux. The phosphoenolpyruvate carboxykinase links the TCA cycle with gluconeogenesis and is essential for B. subtilis growing on gluconeogenic carbon sources. Only under gluconeogenic growth conditions an interaction of these two proteins is detectable and disappears under glycolytic growth conditions. (C) 2010 Elsevier Inc. All rights reserved."],["dc.identifier.doi","10.1016/j.ymben.2010.10.001"],["dc.identifier.isi","000285651100003"],["dc.identifier.pmid","20933603"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/24494"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Academic Press Inc Elsevier Science"],["dc.relation.issn","1096-7176"],["dc.title","Physical interactions between tricarboxylic acid cycle enzymes in Bacillus subtilis: Evidence for a metabolon"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","692"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Molecular Microbiology"],["dc.bibliographiccitation.lastpage","702"],["dc.bibliographiccitation.volume","67"],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Stuelke, Joerg"],["dc.date.accessioned","2018-11-07T11:18:49Z"],["dc.date.available","2018-11-07T11:18:49Z"],["dc.date.issued","2008"],["dc.description.abstract","All regulatory processes require components that sense the environmental or metabolic conditions of the cell, and sophisticated sensory proteins have been studied in great detail. During the last few years, it turned out that enzymes can control gene expression in response to the availability of their substrates. Here, we review four different mechanisms by which these enzymes interfere with regulation in bacteria. First, some enzymes have acquired a DNA-binding domain and act as direct transcription repressors by binding DNA in the absence of their substrates. A second class is represented by aconitase, which can bind iron responsive elements in the absence of iron to control the expression of genes involved in iron homoeostasis. The third class of these enzymes is sugar permeases of the phosphotransferase system that control the activity of transcription regulators by phosphorylating them in the absence of the specific substrate. Finally, a fourth class of regulatory enzymes controls the activity of transcription factors by inhibitory protein-protein interactions. We suggest that the enzymes that are active in the control of gene expression should be designated as trigger enzymes. An analysis of the occurrence of trigger enzymes suggests that the duplication and subsequent functional specialization is a major pattern in their evolution."],["dc.identifier.doi","10.1111/j.1365-2958.2007.06071.x"],["dc.identifier.isi","000253312400003"],["dc.identifier.pmid","18086213"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/55128"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","0950-382X"],["dc.title","Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression"],["dc.type","review"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","171"],["dc.bibliographiccitation.journal","Metabolic Engineering"],["dc.bibliographiccitation.lastpage","179"],["dc.bibliographiccitation.volume","45"],["dc.contributor.author","Reuß, Daniel R."],["dc.contributor.author","Rath, Hermann"],["dc.contributor.author","Thürmer, Andrea"],["dc.contributor.author","Benda, Martin"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Völker, Uwe"],["dc.contributor.author","Mäder, Ulrike"],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Stülke, Jörg"],["dc.date.accessioned","2020-12-10T15:21:49Z"],["dc.date.available","2020-12-10T15:21:49Z"],["dc.date.issued","2018"],["dc.identifier.doi","10.1016/j.ymben.2017.12.004"],["dc.identifier.issn","1096-7176"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/73172"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.title","Changes of DNA topology affect the global transcription landscape and allow rapid growth of a Bacillus subtilis mutant lacking carbon catabolite repression"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","5431"],["dc.bibliographiccitation.issue","19"],["dc.bibliographiccitation.journal","Journal of Bacteriology"],["dc.bibliographiccitation.lastpage","5441"],["dc.bibliographiccitation.volume","193"],["dc.contributor.author","Lehnik-Habrink, Martin"],["dc.contributor.author","Newman, Joseph"],["dc.contributor.author","Rothe, Fabian M."],["dc.contributor.author","Solovyova, Alexandra S."],["dc.contributor.author","Rodrigues, Cecilia"],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Lewis, Richard J."],["dc.contributor.author","Stuelke, Joerg"],["dc.date.accessioned","2018-11-07T08:51:23Z"],["dc.date.available","2018-11-07T08:51:23Z"],["dc.date.issued","2011"],["dc.description.abstract","The control of mRNA stability is an important component of regulation in bacteria. Processing and degradation of mRNAs are initiated by an endonucleolytic attack, and the cleavage products are processively degraded by exoribonucleases. In many bacteria, these RNases, as well as RNA helicases and other proteins, are organized in a protein complex called the RNA degradosome. In Escherichia coli, the RNA degradosome is assembled around the essential endoribonuclease E. In Bacillus subtilis, the recently discovered essential endoribonuclease RNase Y is involved in the initiation of RNA degradation. Moreover, RNase Y interacts with other RNases, the RNA helicase CshA, and the glycolytic enzymes enolase and phosphofructokinase in a degradosome-like complex. In this work, we have studied the domain organization of RNase Y and the contribution of the domains to protein-protein interactions. We provide evidence for the physical interaction between RNase Y and the degradosome partners in vivo. We present experimental and bioinformatic data which indicate that the RNase Y contains significant regions of intrinsic disorder and discuss the possible functional implications of this finding. The localization of RNase Y in the membrane is essential both for the viability of B. subtilis and for all interactions that involve RNase Y. The results presented in this study provide novel evidence for the idea that RNase Y is the functional equivalent of RNase E, even though the two enzymes do not share any sequence similarity."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft [SFB860]; United Kingdom BBSRC"],["dc.identifier.doi","10.1128/JB.05500-11"],["dc.identifier.isi","000294826200042"],["dc.identifier.pmid","21803996"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/21923"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Amer Soc Microbiology"],["dc.relation.issn","0021-9193"],["dc.title","RNase Y in Bacillus subtilis: a Natively Disordered Protein That Is the Functional Equivalent of RNase E from Escherichia coli"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Journal of Bacteriology"],["dc.bibliographiccitation.volume","201"],["dc.contributor.author","Quintana, Ingrid M."],["dc.contributor.author","Gibhardt, Johannes"],["dc.contributor.author","Turdiev, Asan"],["dc.contributor.author","Hammer, Elke"],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Lee, Vincent T."],["dc.contributor.author","Magni, Christian"],["dc.contributor.author","Stülke, Jörg"],["dc.contributor.editor","Stock, Ann M."],["dc.date.accessioned","2020-12-10T18:37:01Z"],["dc.date.available","2020-12-10T18:37:01Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1128/JB.00028-19"],["dc.identifier.eissn","1098-5530"],["dc.identifier.issn","0021-9193"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/76816"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.title","The KupA and KupB Proteins of Lactococcus lactis IL1403 Are Novel c-di-AMP Receptor Proteins Responsible for Potassium Uptake"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","167"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Current Opinion in Microbiology"],["dc.bibliographiccitation.lastpage","172"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Forchhammer, K."],["dc.contributor.author","Stulke, J."],["dc.date.accessioned","2018-11-07T10:01:19Z"],["dc.date.available","2018-11-07T10:01:19Z"],["dc.date.issued","2006"],["dc.description.abstract","The metabolism of carbon- and nitrogen-containing compounds is fundamental to all forms of life. To cope with changing environmental conditions, bacteria have to sense the nutrient supply and adapt their metabolism accordingly. In addition to nutrient- and pathway-specific responses, they integrate information from the different branches of metabolism to coordinate the control of the expression of many metabolic genes. Two major players interconnecting carbon and nitrogen regulation are the PII proteins and the phosphotransferase system. Moreover, several DNA-binding transcription regulators sense signals are derived from both carbon and nitrogen metabolism. The regulatory networks enable the bacteria to make the appropriate metabolic responses to changing nutrient availabilities in the environment."],["dc.identifier.doi","10.1016/j.mib.2006.01.001"],["dc.identifier.isi","000237185900008"],["dc.identifier.pmid","16458044"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/37990"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Current Biology Ltd"],["dc.relation.issn","1369-5274"],["dc.title","Regulatory links between carbon and nitrogen metabolism"],["dc.type","review"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3557"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Journal of Bacteriology"],["dc.bibliographiccitation.lastpage","3564"],["dc.bibliographiccitation.volume","190"],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Gunka, Katrin"],["dc.contributor.author","Landmann, Jens J."],["dc.contributor.author","Stuelke, Joerg"],["dc.date.accessioned","2018-11-07T11:15:36Z"],["dc.date.available","2018-11-07T11:15:36Z"],["dc.date.issued","2008"],["dc.description.abstract","Glutamate is a central metabolite in all organisms since it provides the link between carbon and nitrogen metabolism. In Bacillus subtilis, glutamate is synthesized exclusively by the glutamate synthase, and it can be degraded by the glutamate dehydrogenase. In B. subtilis, the major glutamate dehydrogenase RocG is expressed only in the presence of arginine, and the bacteria are unable to utilize glutamate as the only carbon source. In addition to rocG, a second cryptic gene (gudB) encodes an inactive glutamate dehydrogenase. Mutations in rocG result in the rapid accumulation of gudB1 suppressor mutations that code for an active enzyme. In this work, we analyzed the physiological significance of this constellation of genes and enzymes involved in glutamate metabolism. We found that the weak expression of rocG in the absence of the inducer arginine is limiting for glutamate utilization. Moreover, we addressed the potential ability of the active glutamate dehydrogenases of B. subtilis to synthesize glutamate. Both RocG and GudB1 were unable to catalyze the anabolic reaction, most probably because of their very high K-m values for ammonium. In contrast, the Escherichia coli glutamate dehydrogenase is able to produce glutamate even in the background of a B. subtilis cell. B. subtilis responds to any mutation that interferes with glutamate metabolism with the rapid accumulation of extragenic or intragenic suppressor mutations, bringing the glutamate supply into balance. Similarly, with the presence of a cryptic gene, the system can flexibly respond to changes in the external glutamate supply by the selection of mutations."],["dc.identifier.doi","10.1128/JB.00099-08"],["dc.identifier.isi","000255622500015"],["dc.identifier.pmid","18326565"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/54401"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Amer Soc Microbiology"],["dc.relation.issn","0021-9193"],["dc.title","Glutamate metabolism in Bacillus subtilis: Gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations of the system"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1350"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Molecular & Cellular Proteomics"],["dc.bibliographiccitation.lastpage","1360"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Rothe, Fabian M."],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Wagner, Eva M."],["dc.contributor.author","Hellwig, Daniel"],["dc.contributor.author","Lehnik-Habrink, Martin"],["dc.contributor.author","Hammer, Elke"],["dc.contributor.author","Voelker, Uwe"],["dc.contributor.author","Stuelke, Joerg"],["dc.date.accessioned","2018-11-07T08:29:31Z"],["dc.date.available","2018-11-07T08:29:31Z"],["dc.date.issued","2009"],["dc.description.abstract","Glycolysis is one of the most important metabolic pathways in heterotrophic organisms. Several genes encoding glycolytic enzymes are essential in many bacteria even under conditions when neither glycolytic nor gluconeogenic activities are required. In this study, a screening for in vivo interaction partners of glycolytic enzymes of the soil bacterium Bacillus subtilis was used to provide a rationale for essentiality of glycolytic enzymes. Glycolytic enzymes proved to be in close contact with several other proteins, among them a high proportion of essential proteins. Among these essential interaction partners, other glycolytic enzymes were most prominent. Two-hybrid studies confirmed interactions of phosphofructokinase with phosphoglyceromutase and enolase. Such a complex of glycolytic enzymes might allow direct substrate channeling of glycolytic intermediates. Moreover we found associations of glycolytic enzymes with several proteins known or suspected to be involved in RNA processing and degradation. One of these proteins, Rny (YmdA), which has so far not been functionally characterized, is required for the processing of the mRNA of the glycolytic gapA operon. Two-hybrid analyses confirmed the interactions between the glycolytic enzymes phosphofructokinase and enolase and the enzymes involved in RNA processing, RNase J1, Rny, and polynucleotide phosphorylase. Moreover RNase J1 interacts with its homologue RNase J2. We suggest that this complex of mRNA processing and glycolytic enzymes is the B. subtilis equivalent of the RNA degradosome. Our findings suggest that the functional interaction of glycolytic enzymes with essential proteins may be the reason why they are indispensable. Molecular & Cellular Proteomics 8: 1350-1360, 2009."],["dc.identifier.doi","10.1074/mcp.M800546-MCP200"],["dc.identifier.isi","000266904900015"],["dc.identifier.pmid","19193632"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/16674"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Amer Soc Biochemistry Molecular Biology Inc"],["dc.relation.issn","1535-9476"],["dc.title","Novel Activities of Glycolytic Enzymes in Bacillus subtilis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]