Söding, Johannes

[["dc.bibliographiccitation.issue","15"],["dc.bibliographiccitation.journal","Science Advances"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Luebben, Anna V."],["dc.contributor.author","Bender, Daniel"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Crowther, Lisa M."],["dc.contributor.author","Erven, Ilka"],["dc.contributor.author","Hofmann, Kay"],["dc.contributor.author","Söding, Johannes"],["dc.contributor.author","Klemp, Henry"],["dc.contributor.author","Bellotti, Cristina"],["dc.contributor.author","Stäuble, Andreas"],["dc.contributor.author","Steinfeld, Robert"],["dc.date.accessioned","2022-05-02T08:02:30Z"],["dc.date.available","2022-05-02T08:02:30Z"],["dc.date.issued","2022"],["dc.description.abstract","Genetic CLN5 variants are associated with childhood neurodegeneration and Alzheimer’s disease; however, the molecular function of ceroid lipofuscinosis neuronal protein 5 (Cln5) is unknown. We solved the Cln5 crystal structure and identified a region homologous to the catalytic domain of members of the N1pC/P60 superfamily of papain-like enzymes. However, we observed no protease activity for Cln5; and instead, we discovered that Cln5 and structurally related PPPDE1 and PPPDE2 have efficient cysteine palmitoyl thioesterase ( S -depalmitoylation) activity using fluorescent substrates. Mutational analysis revealed that the predicted catalytic residues histidine-166 and cysteine-280 are critical for Cln5 thioesterase activity, uncovering a new cysteine-based catalytic mechanism for S -depalmitoylation enzymes. Last, we found that Cln5-deficient neuronal progenitor cells showed reduced thioesterase activity, confirming live cell function of Cln5 in setting S -depalmitoylation levels. Our results provide new insight into the function of Cln5, emphasize the importance of S -depalmitoylation in neuronal homeostasis, and disclose a new, unexpected enzymatic function for the N1pC/P60 superfamily of proteins.\r\nCln5 structure reveals thioesterase activity among N1pC/P60 proteins, stressing the role of S -depalmitoylation in neurodegeneration."],["dc.identifier.doi","10.1126/sciadv.abj8633"],["dc.identifier.pmid","35427157"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/107343"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/476"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-561"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","2375-2548"],["dc.relation.workinggroup","RG Gärtner"],["dc.relation.workinggroup","RG Söding (Quantitative and Computational Biology)"],["dc.title","Cln5 represents a new type of cysteine-based S -depalmitoylase linked to neurodegeneration"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3364"],["dc.bibliographiccitation.issue","19"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","3366"],["dc.bibliographiccitation.volume","37"],["dc.contributor.author","Zhang, Ruoshi"],["dc.contributor.author","Mirdita, Milot"],["dc.contributor.author","Levy Karin, Eli"],["dc.contributor.author","Norroy, Clovis"],["dc.contributor.author","Galiez, Clovis"],["dc.contributor.author","Söding, Johannes"],["dc.contributor.editor","Valencia, Alfonso"],["dc.date.accessioned","2022-03-01T11:46:39Z"],["dc.date.available","2022-03-01T11:46:39Z"],["dc.date.issued","2021"],["dc.description.abstract","Abstract Summary SpacePHARER (CRISPR Spacer Phage–Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage–host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein level, optimizing its scores for matching very short sequences, and combining evidence from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes. Availability and implementation SpacePHARER is available as an open-source (GPLv3), user-friendly command-line software for Linux and macOS: https://github.com/soedinglab/spacepharer. Supplementary information Supplementary data are available at Bioinformatics online."],["dc.description.abstract","Abstract Summary SpacePHARER (CRISPR Spacer Phage–Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage–host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein level, optimizing its scores for matching very short sequences, and combining evidence from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes. Availability and implementation SpacePHARER is available as an open-source (GPLv3), user-friendly command-line software for Linux and macOS: https://github.com/soedinglab/spacepharer. Supplementary information Supplementary data are available at Bioinformatics online."],["dc.identifier.doi","10.1093/bioinformatics/btab222"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103746"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","1460-2059"],["dc.relation.issn","1367-4803"],["dc.title","SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","51"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Structural Biology"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Agarwal, Vatsal"],["dc.contributor.author","Remmert, Michael"],["dc.contributor.author","Biegert, Andreas"],["dc.contributor.author","Söding, Johannes"],["dc.date.accessioned","2022-03-01T11:43:59Z"],["dc.date.available","2022-03-01T11:43:59Z"],["dc.date.issued","2008"],["dc.description.abstract","Abstract Background During the last years, methods for remote homology detection have grown more and more sensitive and reliable. Automatic structure prediction servers relying on these methods can generate useful 3D models even below 20% sequence identity between the protein of interest and the known structure (template). When no homologs can be found in the protein structure database (PDB), the user would need to rerun the same search at regular intervals in order to make timely use of a template once it becomes available. Results PDBalert is a web-based automatic system that sends an email alert as soon as a structure with homology to a protein in the user's watch list is released to the PDB database or appears among the sequences on hold. The mail contains links to the search results and to an automatically generated 3D homology model. The sequence search is performed with the same software as used by the very sensitive and reliable remote homology detection server HHpred, which is based on pairwise comparison of Hidden Markov models. Conclusion PDBalert will accelerate the information flow from the PDB database to all those who can profit from the newly released protein structures for predicting the 3D structure or function of their proteins of interest."],["dc.description.abstract","Abstract Background During the last years, methods for remote homology detection have grown more and more sensitive and reliable. Automatic structure prediction servers relying on these methods can generate useful 3D models even below 20% sequence identity between the protein of interest and the known structure (template). When no homologs can be found in the protein structure database (PDB), the user would need to rerun the same search at regular intervals in order to make timely use of a template once it becomes available. Results PDBalert is a web-based automatic system that sends an email alert as soon as a structure with homology to a protein in the user's watch list is released to the PDB database or appears among the sequences on hold. The mail contains links to the search results and to an automatically generated 3D homology model. The sequence search is performed with the same software as used by the very sensitive and reliable remote homology detection server HHpred, which is based on pairwise comparison of Hidden Markov models. Conclusion PDBalert will accelerate the information flow from the PDB database to all those who can profit from the newly released protein structures for predicting the 3D structure or function of their proteins of interest."],["dc.identifier.doi","10.1186/1472-6807-8-51"],["dc.identifier.pii","216"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/102890"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","1472-6807"],["dc.title","PDBalert: automatic, recurrent remote homology tracking and protein structure prediction"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

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[["dc.bibliographiccitation.firstpage","257"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Applied Physics B"],["dc.bibliographiccitation.lastpage","261"],["dc.bibliographiccitation.volume","69"],["dc.contributor.author","Söding, J."],["dc.contributor.author","Guéry-Odelin, D."],["dc.contributor.author","Desbiolles, P."],["dc.contributor.author","Chevy, F."],["dc.contributor.author","Inamori, H."],["dc.contributor.author","Dalibard, J."],["dc.date.accessioned","2022-06-08T07:59:40Z"],["dc.date.available","2022-06-08T07:59:40Z"],["dc.date.issued","2014"],["dc.identifier.doi","10.1007/s003400050805"],["dc.identifier.pii","9900123"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/110824"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-575"],["dc.relation.eissn","1432-0649"],["dc.relation.issn","0946-2171"],["dc.title","Three-body decay of a rubidium Bose–Einstein condensate"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","101"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","EPL"],["dc.bibliographiccitation.lastpage","106"],["dc.bibliographiccitation.volume","20"],["dc.contributor.author","Söding, J."],["dc.contributor.author","Grimm, R"],["dc.contributor.author","Kowalski, J."],["dc.contributor.author","Ovchinnikov, Yu. B"],["dc.contributor.author","Sidorov, A. I"],["dc.date.accessioned","2022-06-08T07:57:21Z"],["dc.date.available","2022-06-08T07:57:21Z"],["dc.date.issued","2007"],["dc.identifier.doi","10.1209/0295-5075/20/2/002"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/110062"],["dc.notes.intern","DOI-Import GROB-575"],["dc.relation.eissn","1286-4854"],["dc.relation.issn","0295-5075"],["dc.title","Observation of the Magneto-Optical Radiation Force by Laser Spectroscopy"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","837"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","BioEssays"],["dc.bibliographiccitation.lastpage","846"],["dc.bibliographiccitation.volume","25"],["dc.contributor.author","Söding, Johannes"],["dc.contributor.author","Lupas, Andrei N."],["dc.date.accessioned","2022-06-08T07:59:36Z"],["dc.date.available","2022-06-08T07:59:36Z"],["dc.date.issued","2003"],["dc.identifier.doi","10.1002/bies.10321"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/110801"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-575"],["dc.relation.issn","0265-9247"],["dc.title","More than the sum of their parts: On the evolution of proteins from peptides"],["dc.title.alternative","Review articles"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e1003914"],["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.issue","11"],["dc.bibliographiccitation.journal","PLoS Genetics"],["dc.bibliographiccitation.lastpage","15"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Meinel, D. M."],["dc.contributor.author","Burkert-Kautzsch, C."],["dc.contributor.author","Kieser, Anja"],["dc.contributor.author","O'Duibhir, E."],["dc.contributor.author","Siebert, M."],["dc.contributor.author","Mayer, A."],["dc.contributor.author","Cramer, P."],["dc.contributor.author","Söding, Johannes"],["dc.contributor.author","Holstege, F. C. P."],["dc.contributor.author","Straesser, K."],["dc.date.accessioned","2017-09-07T11:47:04Z"],["dc.date.available","2017-09-07T11:47:04Z"],["dc.date.issued","2013"],["dc.description.abstract","Messenger RNA (mRNA) synthesis and export are tightly linked, but the molecular mechanisms of this coupling are largely unknown. In Saccharomyces cerevisiae, the conserved TREX complex couples transcription to mRNA export and mediates mRNP formation. Here, we show that TREX is recruited to the transcription machinery by direct interaction of its subcomplex THO with the serine 2-serine 5 (S2/S5) diphosphorylated CTD of RNA polymerase II. S2 and/or tyrosine 1 (Y1) phosphorylation of the CTD is required for TREX occupancy in vivo, establishing a second interaction platform necessary for TREX recruitment in addition to RNA. Genome-wide analyses show that the occupancy of THO and the TREX components Sub2 and Yra1 increases from the 5' to the 3' end of the gene in accordance with the CTD S2 phosphorylation pattern. Importantly, in a mutant strain, in which TREX is recruited to genes but does not increase towards the 3' end, the expression of long transcripts is specifically impaired. Thus, we show for the first time that a 5'-3' increase of a protein complex is essential for correct expression of the genome. In summary, we provide insight into how the phospho-code of the CTD directs mRNP formation and export through TREX recruitment."],["dc.identifier.doi","10.1371/journal.pgen.1003914"],["dc.identifier.gro","3142255"],["dc.identifier.isi","000330369000015"],["dc.identifier.pmid","24244187"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/6254"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","1553-7404"],["dc.title","Recruitment of TREX to the Transcription Machinery by Its Direct Binding to the Phospho-CTD of RNA Polymerase II"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2517"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Physical Review. A"],["dc.bibliographiccitation.lastpage","2527"],["dc.bibliographiccitation.volume","50"],["dc.contributor.author","Söding, J."],["dc.contributor.author","Grimm, R."],["dc.date.accessioned","2022-06-08T07:59:14Z"],["dc.date.available","2022-06-08T07:59:14Z"],["dc.date.issued","1994"],["dc.identifier.doi","10.1103/PhysRevA.50.2517"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/110680"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-575"],["dc.relation.eissn","1094-1622"],["dc.relation.issn","1050-2947"],["dc.title","Stimulated magneto-optical force in the dressed-atom picture"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","25"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Europhysics Letters (EPL)"],["dc.bibliographiccitation.lastpage","30"],["dc.bibliographiccitation.volume","44"],["dc.contributor.author","Guéry-Odelin, D"],["dc.contributor.author","Söding, J"],["dc.contributor.author","Desbiolles, P"],["dc.contributor.author","Dalibard, J"],["dc.date.accessioned","2022-06-08T07:57:22Z"],["dc.date.available","2022-06-08T07:57:22Z"],["dc.date.issued","2007"],["dc.identifier.doi","10.1209/epl/i1998-00425-9"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/110071"],["dc.notes.intern","DOI-Import GROB-575"],["dc.relation.eissn","1286-4854"],["dc.relation.issn","0295-5075"],["dc.title","Is Bose-Einstein condensation of atomic cesium possible?"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]