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","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","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.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"]]

[["dc.bibliographiccitation.firstpage","642"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Molecular Microbiology"],["dc.bibliographiccitation.lastpage","654"],["dc.bibliographiccitation.volume","65"],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Tripal, Philipp"],["dc.contributor.author","Valerius, Oliver"],["dc.contributor.author","Stuelke, Joerg"],["dc.date.accessioned","2018-11-07T11:00:19Z"],["dc.date.available","2018-11-07T11:00:19Z"],["dc.date.issued","2007"],["dc.description.abstract","Glutamate synthesis is the link between carbon and nitrogen metabolism. In Bacillus subtilis, glutamate is exclusively synthesized by the glutamate synthase encoded by the gltAB operon. The glutamate dehydrogenase RocG from B. subtilis is exclusively devoted to glutamate degradation rather than to its synthesis. The expression of the gltAB operon Is induced by glucose and ammonium and strongly repressed by arginine. Regulation by glucose and arginine depends on the transcriptional activator protein GltC. The gltAB operon is constitutively expressed in a rocG mutant strain, but the molecular mechanism of negative control of gltAB expression by RocG has so far remained unknown. We studied the role of RocG in the intracellular accumulation of GltC. Furthermore, we considered the possibility that RocG might act as a transcription factor and be able to inhibit the expression of gltAB either by binding to the mRNA or to the promoter region of the gltAB operon. Finally, we asked whether a direct binding of RocG to GltC could be responsible for the inhibition of GItC. The genetic and biochemical data presented here show that the glutamate dehydrogenase RocG is able to bind to and concomitantly inactivate the activator protein GItC. This regulatory mechanism by the bifunctional enzyme RocG allows the tight control of glutamate metabolism by the availability of carbon and nitrogen sources."],["dc.identifier.doi","10.1111/j.1365-2958.2007.05816.x"],["dc.identifier.isi","000248484000005"],["dc.identifier.pmid","17608797"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/50896"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Blackwell Publishing"],["dc.relation.issn","0950-382X"],["dc.title","A regulatory protein-protein interaction governs glutamate biosynthesis in Bacillus subtilis: the glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","815"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Journal of Molecular Biology"],["dc.bibliographiccitation.lastpage","827"],["dc.bibliographiccitation.volume","400"],["dc.contributor.author","Gunka, Katrin"],["dc.contributor.author","Newman, Joseph A."],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Rodrigues, Cecilia"],["dc.contributor.author","Hewitt, Lorraine"],["dc.contributor.author","Lewis, Richard J."],["dc.contributor.author","Stuelke, Joerg"],["dc.date.accessioned","2018-11-07T08:41:18Z"],["dc.date.available","2018-11-07T08:41:18Z"],["dc.date.issued","2010"],["dc.description.abstract","Any signal transduction requires communication between a sensory component and an effector. Some enzymes engage in signal perception and transduction, as well as in catalysis, and these proteins are known as \"trigger\" enzymes. In this report, we detail the trigger properties of RocG, the glutamate dehydrogenase of Bacillus subtilis. RocG not only deaminates the key metabolite glutamate to form alpha-ketoglutarate but also interacts directly with GltC, a LysR-type transcription factor that regulates glutamate biosynthesis from alpha-ketoglutarate, thus linking the two metabolic pathways. We have isolated mutants of RocG that separate the two functions. Several mutations resulted in permanent inactivation of GltC as long as a source of glutamate was present. These RocG proteins have lost their ability to catabolize glutamate due to a strongly reduced affinity for glutamate. The second class of mutants is exemplified by the replacement of aspartate residue 122 by asparagine. This mutant protein has retained enzymatic activity but has lost the ability to control the activity of GltC. Crystal structures of glutamate dehydrogenases that permit a molecular explanation of the properties of the various mutants are presented. Specifically, we may propose that D122N replacement affects the surface of RocG. Our data provide evidence for a correlation between the enzymatic activity of RocG and its ability to inactivate GltC, and thus give insights into the mechanism that couples the enzymatic activity of a trigger enzyme to its regulatory function. (C) 2010 Elsevier Ltd. All rights reserved."],["dc.identifier.doi","10.1016/j.jmb.2010.05.055"],["dc.identifier.isi","000280652300014"],["dc.identifier.pmid","20630473"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/19436"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Academic Press Ltd- Elsevier Science Ltd"],["dc.relation.issn","0022-2836"],["dc.title","Functional Dissection of a Trigger Enzyme: Mutations of the Bacillus subtilis Glutamate Dehydrogenase RocG That Affect Differentially Its Catalytic Activity and Regulatory Properties"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","4032"],["dc.bibliographiccitation.issue","22"],["dc.bibliographiccitation.journal","PROTEOMICS"],["dc.bibliographiccitation.lastpage","4035"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Weidinger, Lope Andres Florez"],["dc.contributor.author","Doerrbecker, Bastian"],["dc.contributor.author","Huebner, Sebastian"],["dc.contributor.author","Stuelke, Joerg"],["dc.contributor.author","Commichau, Fabian M."],["dc.date.accessioned","2018-11-07T10:57:30Z"],["dc.date.available","2018-11-07T10:57:30Z"],["dc.date.issued","2007"],["dc.description.abstract","The detection and analysis of protein-protein interactions is one of the central tasks of proteomics in the postgenomic era. For this purpose, we present a procedure, the Strep-protein interaction experiment (SPINE) that combines the advantages of the Strep-tag protein purification system with those of reversible in vivo protein crosslinking by formaldehyde. Using two Bacillus subtilis regulator proteins, we demonstrate that this method is well suited to isolate protein complexes with high purity and virtually no background. Plasmids allowing the high-level expression of proteins carrying an N- or C-terminal Strep-tag in B. subtilis were constructed."],["dc.identifier.doi","10.1002/pmic.200700491"],["dc.identifier.isi","000251293000001"],["dc.identifier.pmid","17994626"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/50267"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-v C H Verlag Gmbh"],["dc.relation.issn","1615-9853"],["dc.title","SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","eaal3011"],["dc.bibliographiccitation.issue","475"],["dc.bibliographiccitation.journal","Science Signaling"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Gundlach, Jan"],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Kaever, Volkhard"],["dc.contributor.author","Gunka, Katrin"],["dc.contributor.author","Hoffmann, Tamara"],["dc.contributor.author","Weiss, Martin"],["dc.contributor.author","Gibhardt, Johannes"],["dc.contributor.author","Thuermer, Andrea"],["dc.contributor.author","Hertel, Dietrich"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Bremer, Erhard"],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Stulke, Joerg"],["dc.date.accessioned","2018-11-07T10:24:56Z"],["dc.date.available","2018-11-07T10:24:56Z"],["dc.date.issued","2017"],["dc.description.abstract","The second messenger cyclic di-adenosine monophosphate (c-di-AMP) is essential in the Gram-positive model organism Bacillus subtilis and in related pathogenic bacteria. It controls the activity of the conserved ydaO riboswitch and of several proteins involved in potassium (K+) uptake. We found that the YdaO protein was conserved among several different bacteria and provide evidence that YdaO functions as a K+ transporter. Thus, we renamed the gene and protein KimA (K+ importer A). Reporter activity assays indicated that expression beyond the c-di-AMP-responsive riboswitch of the kimA upstream regulatory region occurred only in bacteria grown in medium containing low K+ concentrations. Furthermore, mass spectrometry analysis indicated that c-di-AMP accumulated in bacteria grown in the presence of high K+ concentrations but not in low concentrations. A bacterial strain lacking all genes encoding c-di-AMP-synthesizing enzymes was viable when grown in medium containing low K+ concentrations, but not at higher K+ concentrations unless it acquired suppressor mutations in the gene encoding the cation exporter NhaK. Thus, our results indicated that the control of potassium homeostasis is an essential function of c-di-AMP."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft [SPP1879]"],["dc.identifier.doi","10.1126/scisignal.aal3011"],["dc.identifier.isi","000400128400003"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/42751"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Amer Assoc Advancement Science"],["dc.relation.issn","1937-9145"],["dc.relation.issn","1945-0877"],["dc.title","Control of potassium homeostasis is an essential function of the second messenger cyclic di-AMP in Bacillus subtilis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]