Stülke, Jörg

[["dc.bibliographiccitation.artnumber","1492"],["dc.bibliographiccitation.journal","Frontiers in Microbiology"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Cascante-Estepa, Nora"],["dc.contributor.author","Gunka, Katrin"],["dc.contributor.author","Stuelke, Joerg"],["dc.date.accessioned","2018-11-07T10:08:26Z"],["dc.date.available","2018-11-07T10:08:26Z"],["dc.date.issued","2016"],["dc.description.abstract","In bacteria, the control of mRNA stability is crucial to allow rapid adaptation to changing conditions. In most bacteria, RNA degradation is catalyzed by the RNA degradosome, a protein complex composed of endo- and exoribonucleases, RNA helicases, and accessory proteins. In the Gram-positive model organism Bacillus subtilis, the existence of a RNA degradosome assembled around the membrane-bound endoribonuclease RNase Y has been proposed. Here, we have studied the intracellular localization of the protein that have been implicated in the potential B. subtilis RNA degradosome, i.e., polynucleotide phosphorylase, the exoribonucleases J1 and J2, the DEAD-box RNA helicase CshA, and the glycolytic enzymes enolase and phosphofructokinase. Our data suggests that the bulk of these enzymes is located in the cytoplasm. The RNases J1 and J2 as well as the RNA helicase CshA were mainly localized in the peripheral regions of the cell where also the bulk of messenger RNA is localized. We were able to demonstrate active exclusion of these proteins from the transcribing nucleoid. Taken together, our findings suggest that the interactions of the enzymes involved in RNA degradation in B. subtilis are rather transient."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2016"],["dc.identifier.doi","10.3389/fmicb.2016.01492"],["dc.identifier.isi","000383647300001"],["dc.identifier.pmid","27708634"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13776"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/39460"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Frontiers Media Sa"],["dc.relation.issn","1664-302X"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Localization of Components of the RNA-Degrading Machine in Bacillus subtilis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","1328"],["dc.bibliographiccitation.journal","Frontiers in microbiology"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Blötz, Cedric"],["dc.contributor.author","Treffon, Katrin"],["dc.contributor.author","Kaever, Volkhard"],["dc.contributor.author","Schwede, Frank"],["dc.contributor.author","Hammer, Elke"],["dc.contributor.author","Stülke, Jörg"],["dc.date.accessioned","2019-07-09T11:43:38Z"],["dc.date.available","2019-07-09T11:43:38Z"],["dc.date.issued","2017"],["dc.description.abstract","Bacteria often use cyclic dinucleotides as second messengers for signal transduction. While the classical molecule c-di-GMP is involved in lifestyle selection, the functions of the more recently discovered signaling nucleotide cyclic di-AMP are less defined. For many Gram-positive bacteria, c-di-AMP is essential for growth suggesting its involvement in a key cellular function. We have analyzed c-di-AMP signaling in the genome-reduced pathogenic bacterium Mycoplasma pneumoniae. Our results demonstrate that these bacteria produce c-di-AMP, and we could identify the diadenylate cyclase CdaM (MPN244). This enzyme is the founding member of a novel family of diadenylate cyclases. Of two potential c-di-AMP degrading phosphodiesterases, only PdeM (MPN549) is active in c-di-AMP degradation, whereas NrnA (MPN140) was reported to degrade short oligoribonucleotides. As observed in other bacteria, both the c-di-AMP synthesizing and the degrading enzymes are essential for M. pneumoniae suggesting control of a major homeostatic process. To obtain more insights into the nature of this process, we have identified a c-di-AMP-binding protein from M. pneumoniae, KtrC. KtrC is the cytoplasmic regulatory subunit of the low affinity potassium transporter KtrCD. It is established that binding of c-di-AMP inhibits the KtrCD activity resulting in a limitation of potassium uptake. Our results suggest that the control of potassium homeostasis is the essential function of c-di-AMP in M. pneumoniae."],["dc.identifier.doi","10.3389/fmicb.2017.01328"],["dc.identifier.pmid","28751888"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/14609"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/58934"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1664-302X"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.subject.ddc","570"],["dc.title","Identification of the Components Involved in Cyclic Di-AMP Signaling in Mycoplasma pneumoniae"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","6102"],["dc.bibliographiccitation.issue","21"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","6115"],["dc.bibliographiccitation.volume","34"],["dc.contributor.author","Schilling, Oliver"],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Hertrich, Tina"],["dc.contributor.author","Voersmann, Hanna"],["dc.contributor.author","Jessen, Dirk"],["dc.contributor.author","Huebner, Sebastian"],["dc.contributor.author","Titgemeyer, Fritz"],["dc.contributor.author","Stuelke, Joerg"],["dc.date.accessioned","2018-11-07T08:55:16Z"],["dc.date.available","2018-11-07T08:55:16Z"],["dc.date.issued","2006"],["dc.description.abstract","Regulatory systems often evolve by duplication of ancestral systems and subsequent specialization of the components of the novel signal transduction systems. In the Gram-positive soil bacterium Bacillus subtilis, four homologous antitermination systems control the expression of genes involved in the metabolism of glucose, sucrose and beta-glucosides. Each of these systems is made up of a sensory sugar permease that does also act as phosphotransferase, an antitermination protein, and a RNA switch that is composed of two mutually exclusive structures, a RNA antiterminator (RAT) and a transcriptional terminator. We have studied the contributions of sugar specificity of the permeases, carbon catabolite repression, and protein-RAT recognition for the straightness of the signalling chains. We found that the beta-glucoside permease BglP does also have a minor activity in glucose transport. However, this activity is irrelevant under physiological conditions since carbon catabolite repression in the presence of glucose prevents the synthesis of the beta-glucoside permease. Reporter gene studies, in vitro RNA-protein interaction analyzes and northern blot transcript analyzes revealed that the interactions between the antiterminator proteins and their RNA targets are the major factor contributing to regulatory specificity. Both structural features in the RATs and individual bases are important specificity determinants. Our study revealed that the specificity of protein-RNA interactions, substrate specificity of the permeases as well as the general mechanism of carbon catabolite repression together allow to keep the signalling chains straight and to avoid excessive cross-talk between the systems."],["dc.identifier.doi","10.1093/nar/gkl733"],["dc.identifier.isi","000242716800010"],["dc.identifier.pmid","17074746"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?goescholar/4130"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/22869"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","0305-1048"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","Keeping signals straight in transcription regulation: specificity determinants for the interaction of a family of conserved bacterial RNA-protein couples"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","5231"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","5242"],["dc.bibliographiccitation.volume","47"],["dc.contributor.author","Reuß, Daniel R"],["dc.contributor.author","Faßhauer, Patrick"],["dc.contributor.author","Mroch, Philipp Joel"],["dc.contributor.author","Ul-Haq, Inam"],["dc.contributor.author","Koo, Byoung-Mo"],["dc.contributor.author","Pöhlein, Anja"],["dc.contributor.author","Gross, Carol A"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Brantl, Sabine"],["dc.contributor.author","Stülke, Jörg"],["dc.date.accessioned","2020-12-10T18:19:35Z"],["dc.date.available","2020-12-10T18:19:35Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1093/nar/gkz260"],["dc.identifier.eissn","1362-4962"],["dc.identifier.issn","0305-1048"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16450"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/75305"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY-NC 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc/4.0"],["dc.title","Topoisomerase IV can functionally replace all type 1A topoisomerases in Bacillus subtilis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2853"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","NUCLEIC ACIDS RESEARCH"],["dc.bibliographiccitation.lastpage","2864"],["dc.bibliographiccitation.volume","32"],["dc.contributor.author","Schilling, Oliver"],["dc.contributor.author","Langbein, Ines"],["dc.contributor.author","Müller, Michael"],["dc.contributor.author","Schmalisch, Matthias H."],["dc.contributor.author","Stülke, Jörg"],["dc.date.accessioned","2019-07-10T08:12:53Z"],["dc.date.available","2019-07-10T08:12:53Z"],["dc.date.issued","2004"],["dc.description.abstract","The Gram-positive soil bacterium Bacillus subtilis transports glucose by the phosphotransferase system. The genes for this system are encoded in the ptsGHI operon. The expression of this operon is controlled at the level of transcript elongation by a protein-dependent riboswitch. In the absence of glucose a transcriptional terminator prevents elongation into the structural genes. In the presence of glucose, the GlcT protein is activated and binds and stabilizes an alternative RNA structure that overlaps the terminator and prevents termination. In this work, we have studied the structural and sequence requirements for the two mutually exclusive RNA structures, the terminator and the RNA antiterminator (the RAT sequence). In both cases, the structure seems to be more important than the actual sequence. The number of paired and unpaired bases in the RAT sequence is essential for recognition by the antiterminator protein GlcT. In contrast, mutations of individual bases are well tolerated as long as the general structure of the RAT is not impaired. The introduction of one additional base in the RAT changed its structure and resulted in complete loss of interaction with GlcT. In contrast, this mutant RAT was efficiently recognized by a different B.subtilis antitermination protein, LicT."],["dc.identifier.fs","28429"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?goescholar/4114"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/61066"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","0305-1048"],["dc.relation.issn","1362-4962"],["dc.relation.orgunit","Fakultät für Biologie und Psychologie"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject.ddc","570"],["dc.title","A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillus subtilis: RNA structure rather than sequence provides interaction specificity."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","804"],["dc.bibliographiccitation.journal","Frontiers in Microbiology"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Gundlach, Jan"],["dc.contributor.author","Rath, Hermann"],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Maeder, Ulrike"],["dc.contributor.author","Stuelke, Joerg"],["dc.date.accessioned","2018-11-07T10:14:07Z"],["dc.date.available","2018-11-07T10:14:07Z"],["dc.date.issued","2016"],["dc.description.abstract","The Gram-positive model organism Bacillus subtilis produces the essential second messenger signaling nucleotide cyclic di-AMP. In B. subtilis and other bacteria, c-di-AMP has been implicated in diverse functions such as control of metabolism, cell division and cell wall synthesis, and potassium transport. To enhance our understanding of the multiple functions of this second messenger, we have studied the consequences of c-di-AMP accumulation at a global level by a transcriptome analysis. C-di-AMP accumulation affected the expression of about 700 genes, among them the two major operons required for biofilm formation. The expression of both operons was severely reduced both in the laboratory and a non-domesticated strain upon accumulation of c-di-AMP. In excellent agreement, the corresponding strain was unable to form complex colonies. In B. subtilis, the transcription factor SinR controls the expression of biofilm genes by binding to their promoter regions resulting in transcription repression. Inactivation of the sing gene restored biofilm formation even at high intracellular c-di-AMP concentrations suggesting that the second messenger acts upstream of SinR in the signal transduction pathway. As c-di-AMP accumulation did not affect the intracellular levels of SinR, we conclude that the nucleotide affects the activity of SinR."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2016"],["dc.identifier.doi","10.3389/fmicb.2016.00804"],["dc.identifier.isi","000376484900001"],["dc.identifier.pmid","27252699"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13293"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/40564"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Frontiers Media Sa"],["dc.relation.issn","1664-302X"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Second Messenger Signaling in Bacillus subtilis: Accumulation of Cyclic di-AMP Inhibits Biofilm Formation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","143"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Cell Systems"],["dc.bibliographiccitation.lastpage","158.e13"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Yus, Eva"],["dc.contributor.author","Lloréns-Rico, Verónica"],["dc.contributor.author","Martínez, Sira"],["dc.contributor.author","Gallo, Carolina"],["dc.contributor.author","Eilers, Hinnerk"],["dc.contributor.author","Blötz, Cedric"],["dc.contributor.author","Stülke, Jörg"],["dc.contributor.author","Lluch-Senar, Maria"],["dc.contributor.author","Serrano, Luis"],["dc.date.accessioned","2020-12-10T14:23:03Z"],["dc.date.available","2020-12-10T14:23:03Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1016/j.cels.2019.07.001"],["dc.identifier.issn","2405-4712"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16409"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/71814"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY-NC-ND 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc-nd/4.0"],["dc.title","Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","500"],["dc.bibliographiccitation.journal","Frontiers in Microbiology"],["dc.bibliographiccitation.volume","6"],["dc.contributor.author","Grangeasse, Christophe"],["dc.contributor.author","Mijakovic, Ivan"],["dc.contributor.author","Stülke, Jörg"],["dc.date.accessioned","2018-11-07T09:57:00Z"],["dc.date.available","2018-11-07T09:57:00Z"],["dc.date.issued","2015"],["dc.identifier.doi","10.3389/fmicb.2015.00500"],["dc.identifier.isi","000356292600001"],["dc.identifier.pmid","26074895"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/37075"],["dc.language.iso","en"],["dc.notes.intern","DeepGreen Import"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Frontiers Media S.A."],["dc.relation.eissn","1664-302X"],["dc.relation.issn","1664-302X"],["dc.rights","http://creativecommons.org/licenses/by/4.0/"],["dc.title","Regulatory potential of post-translational modifications in bacteria"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.subtype","letter_note"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e1009092"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","PLoS Genetics"],["dc.bibliographiccitation.volume","17"],["dc.contributor.author","Krüger, Larissa"],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Rath, Hermann"],["dc.contributor.author","Pedreira, Tiago"],["dc.contributor.author","Ischebeck, Till"],["dc.contributor.author","Poehlein, Anja"],["dc.contributor.author","Gundlach, Jan"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Völker, Uwe"],["dc.contributor.author","Mäder, Ulrike"],["dc.contributor.author","Stülke, Jörg"],["dc.date.accessioned","2021-04-14T08:29:55Z"],["dc.date.available","2021-04-14T08:29:55Z"],["dc.date.issued","2021"],["dc.description.sponsorship","Open-Access-Publikationsfonds 2021"],["dc.identifier.doi","10.1371/journal.pgen.1009092"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/83034"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation.eissn","1553-7404"],["dc.rights","CC BY 4.0"],["dc.title","Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","4360"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","4372"],["dc.bibliographiccitation.volume","39"],["dc.contributor.author","Huebner, Sebastian"],["dc.contributor.author","Declerck, Nathalie"],["dc.contributor.author","Diethmaier, Christine"],["dc.contributor.author","Le Coq, Dominique"],["dc.contributor.author","Aymerich, Stephane"],["dc.contributor.author","Stuelke, Joerg"],["dc.date.accessioned","2018-11-07T08:56:21Z"],["dc.date.available","2018-11-07T08:56:21Z"],["dc.date.issued","2011"],["dc.description.abstract","Each family of signal transduction systems requires specificity determinants that link individual signals to the correct regulatory output. In Bacillus subtilis, a family of four anti-terminator proteins controls the expression of genes for the utilisation of alternative sugars. These regulatory systems contain the anti-terminator proteins and a RNA structure, the RNA anti-terminator (RAT) that is bound by the anti-terminator proteins. We have studied three of these proteins (SacT, SacY, and LicT) to understand how they can transmit a specific signal in spite of their strong structural homology. A screen for random mutations that render SacT capable to bind a RNA structure recognized by LicT only revealed a substitution (P26S) at one of the few non-conserved residues that are in contact with the RNA. We have randomly modified this position in SacT together with another non-conserved RNA-contacting residue (Q31). Surprisingly, the mutant proteins could bind all RAT structures that are present in B. subtilis. In a complementary approach, reciprocal amino acid exchanges have been introduced in LicT and SacY at non-conserved positions of the RNA-binding site. This analysis revealed the key role of an arginine side-chain for both the high affinity and specificity of LicT for its cognate RAT. Introduction of this Arg at the equivalent position of SacY (A26) increased the RNA binding in vitro but also resulted in a relaxed specificity. Altogether our results suggest that this family of anti-termination proteins has evolved to reach a compromise between RNA binding efficacy and specific interaction with individual target sequences."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft; Fonds der Chemischen Industrie"],["dc.identifier.doi","10.1093/nar/gkr021"],["dc.identifier.isi","000291063500036"],["dc.identifier.pmid","21278164"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/8747"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/23128"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","0305-1048"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","Prevention of cross-talk in conserved regulatory systems: identification of specificity determinants in RNA-binding anti-termination proteins of the BglG family"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]