Bibliography of the Universität Regensburg

Hanelt, Tiana Nicole, Treiber, Nora, Treiber, Thomas, Lehmann, Gerhard, Eichner, Norbert, Rothmeier, Tamara, Schmid, Georg, Reichelt, Robert, Zambelli, Federico, Pavesi, Giulio, Grohmann, Dina and Meister, Gunter (2024) Endo-bind-n-seq: identifying RNA motifs of RNA binding proteins isolated from endogenous sources. Life Science Alliance 8 (2), e202402782.

Stöckl, Richard , Nißl, Laura, Reichelt, Robert, Rachel, Reinhard, Grohmann, Dina and Grünberger, Felix (2023) The transcriptional regulator EarA and intergenic terminator sequences modulate archaellation in Pyrococcus furiosus. Frontiers in Microbiology 14.

Grünberger, Felix , Schmidt, Georg, El Ahmad, Zubeir, Fenk, Martin, Vogl, Katharina, Reichelt, Robert Martin , Hausner, Winfried , Urlaub, Henning, Lenz, Christof, Grohmann, Dina , Vogel, Joerg and Dong, Xiuzhu (2023) Uncovering the temporal dynamics and regulatory networks of thermal stress response in a hyperthermophile using transcriptomics and proteomics. mBio.

Seeholzer, Theresa, Tarau, Daniela , Hollendonner, Lea, Auer, Andrea , Rachel, Reinhard, Grohmann, Dina , Giessibl, Franz J. and Weymouth, Alfred J. (2023) A Next-Generation qPlus-Sensor-Based AFM Setup: Resolving Archaeal S-Layer Protein Structures in Air and Liquid. The Journal of Physical Chemistry B 127 (31), pp. 6949-6957. Fulltext restricted.

Grünberger, Felix , Jüttner, Michael, Knüppel, Robert Michael, Ferreira-Cerca, Sébastien and Grohmann, Dina (2023) Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea. RNA 29 (8), pp. 1255-1273.

Dengler, Linda , Meier, Julia, Klingl, Andreas, Nißl, Laura, Bellack, Annett , Grohmann, Dina , Rachel, Reinhard and Huber, Harald (2023) A novel interdomain consortium from a Costa Rican oil well composed of Methanobacterium cahuitense sp. nov. and Desulfomicrobium aggregans sp. nov. Archives of Microbiology 205 (5).

Eckl, Daniel Bernhard , Hoffmann, Anja Karen, Landgraf, Nicole, Kalb, Larissa, Bäßler, Pauline, Wallner, Susanne, Eichner, Anja, Huber, Harald , Hackbarth, Steffen and Bäumler, Wolfgang (2023) Photodynamic inactivation of different pathogenic bacteria on human skin using a novel photosensitizer hydrogel. Journal of the European Academy of Dermatology and Venereology.

Höllerer, Simon and Jeschek, Markus (2023) Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript. Nucleic Acids Research 51 (5), pp. 2377-2396.

Agam, Ganesh , Gebhardt, Christian, Popara, Milana , Mächtel, Rebecca, Folz, Julian, Ambrose, Benjamin, Chamachi, Neharika , Chung, Sang Yoon , Craggs, Timothy D. , de Boer, Marijn, Grohmann, Dina, Ha, Taekjip, Hartmann, Andreas , Hendrix, Jelle, Hirschfeld, Verena, Hübner, Christian G., Hugel, Thorsten, Kammerer, Dominik, Kang, Hyun-Seo, Kapanidis, Achillefs N., Krainer, Georg, Kramm, Kevin, Lemke, Edward A., Lerner, Eitan , Margeat, Emmanuel , Martens, Kirsten, Michaelis, Jens , Mitra, Jaba, Moya Muñoz, Gabriel G., Quast, Robert B. , Robb, Nicole C., Sattler, Michael , Schlierf, Michael , Schneider, Jonathan, Schröder, Tim, Sefer, Anna, Tan, Piau Siong, Thurn, Johann, Tinnefeld, Philip, van Noort, John, Weiss, Shimon, Wendler, Nicolas, Zijlstra, Niels, Barth, Anders , Seidel, Claus A. M., Lamb, Don C. and Cordes, Thorben (2023) Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins. Nature Methods 20 (4), pp. 523-535. Fulltext not available.

Reichelt, Robert, Rothmeier, Tamara, Grünberger, Felix, Willkomm, Sarah, Bruckmann, Astrid, Hausner, Winfried and Grohmann, Dina (2023) The archaeal Lsm protein from Pyrococcus furiosus binds co-transcriptionally to poly(U)-rich target RNAs. Biological Chemistry 404 (11-12), pp. 1085-1100. Fulltext not available.

Wörle, Elisabeth Johanna Viera (2022) Cas12a is governed in its Activity and Conformational Transitions by the Two Interplaying Key Elements Helix 1 and Bridge Helix. PhD, Universität Regensburg.

Wörle, Elisabeth, Newman, Anthony, D’Silva, Jovita, Burgio, Gaetan and Grohmann, Dina (2022) Allosteric activation of CRISPR-Cas12a requires the concerted movement of the bridge helix and helix 1 of the RuvC II domain. Nucleic Acids Research 50 (17), pp. 10153-10168.

Dengler, Linda , Meier, Julia, Grünberger, Felix , Bellack, Annett , Rachel, Reinhard , Grohmann, Dina and Huber, Harald (2022) Methanofollis propanolicus sp. nov., a novel archaeal isolate from a Costa Rican oil well that uses propanol for methane production. Archives of Microbiology 204 (9).

Willkomm, Sarah , Jakob, Leonhard, Kramm, Kevin, Graus, Veronika, Neumeier, Julia, Meister, Gunter and Grohmann, Dina (2022) Single-molecule FRET uncovers hidden conformations and dynamics of human Argonaute 2. Nature Communications 13, art.no.3825.

Buriánková, Iva, Molíková, Anna , Vítězová, Monika , Onderka, Vladimír, Vítěz, Tomáš, Urbanová, Iva, Hanišáková, Nikola , Černý, Martin , Novák, David , Lochman, Jan, Zeman, Josef, Javůrek, Jakub, Machálková, Markéta, Dengler, Linda and Huber, Harald (2022) Microbial Communities in Underground Gas Reservoirs Offer Promising Biotechnological Potential. Fermentation 8 (6), p. 251. Fulltext not available.

Grünberger, Felix, Ferreira-Cerca, Sébastien and Grohmann, Dina (2021) Nanopore sequencing of RNA and cDNA molecules in Escherichia coli. RNA 28 (3), pp. 400-417.

Gust, Alexander (2021) Entwicklung neuer einzelmolekülspektroskopischer Methoden zur Analyse biomolekularer Komplexe im RNA silencing Prozess. PhD, Universität Regensburg.

Grohmann, Dina, Weixlbaumer, Albert, Grünberger, Felix and Werner, Finn (2021) Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World. Frontiers in Microbiology 2021 (12), p. 661827. (Submitted)

Grünberger, Felix, Reichelt, Robert, Waege, Ingrid, Ned, Verena, Bronner, Korbinian, Kaljanac, Marcell, Weber, Nina, El Ahmad, Zubeir, Knauss, Lena, Madej, M. Gregor , Ziegler, Christine, Grohmann, Dina and Hausner, Winfried (2021) CopR, a Global Regulator of Transcription to Maintain Copper Homeostasis in Pyrococcus furiosus. Frontiers in Microbiology 11 (613532), pp. 1-18.

Wörle, Elisabeth, Jakob, Leonhard, Schmidbauer, Andreas, Zinner, Gabriel and Grohmann, Dina (2021) Decoupling the bridge helix of Cas12a results in a reduced trimming activity, increased mismatch sensitivity and impaired conformational transitions. Nucleic Acids Research 49 (9), pp. 5278-5293. Fulltext not available.

Aldag, Pierre, Welzel, Fabian, Jakob, Leonhard, Schmidbauer, Andreas, Rutkauskas, Marius, Fettes, Fergus, Grohmann, Dina and Seidel, Ralf (2021) Probing the stability of the SpCas9–DNA complex after cleavage. Nucleic Acids Research 49 (21), pp. 12411-12421. Fulltext not available.

Kramm, Kevin Oliver (2020) Single-molecule analysis of transcription initiation in archaea and eukaryotes. PhD, Universität Regensburg.

Kramm, Kevin, Schröder, Tim, Gouge, Jerome , Vera, Andrés Manuel , Gupta, Kapil , Heiss, Florian B. , Liedl, Tim , Engel, Christoph, Berger, Imre , Vannini, Alessandro , Tinnefeld, Philip and Grohmann, Dina (2020) DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability. Nature Communications 11 (2828), pp. 1-12.

Willkomm, Sarah, Moissl, Benedikt, Michel, Henri and Grohmann, Dina (2020) Die erstaunliche Vielseitigkeit der Argonauten-Crew. Biospektrum 26, pp. 603-605.

Buckley, Ryan J., Kramm, Kevin, Cooper, Christopher D. O. , Grohmann, Dina and Bolt, Edward L. (2020) Mechanistic insights into Lhr helicase function in DNA repair. Biochemical Journal 477 (16), pp. 2935-2947. Fulltext not available.

Grünberger, Felix, Reichelt, Robert Martin , Bunk, Boyke, Spröer, Cathrin, Overmann, Jörg, Rachel, Reinhard , Grohmann, Dina and Hausner, Winfried (2019) Next Generation DNA-Seq and Differential RNA-Seq Allow Re-annotation of the Pyrococcus furiosus DSM 3638 Genome and Provide Insights Into Archaeal Antisense Transcription. Frontiers in Microbiology 2019 (10), p. 1603.

Kreuter, Lydia J., Weinfurtner, Andrea, Ziegler, Alexander, Weigl, Julia, Hoffmann, Jan, Morgner, Nina, Müller, Volker, Huber, Harald and Metcalf, William W. (2019) Purification of a Crenarchaeal ATP Synthase in the Light of the Unique Bioenergetics of Ignicoccus Species. Journal of Bacteriology 201 (7). Fulltext not available.

Reichelt-Wurm, Simone, Wirtz, Tobias, Chittka, Dominik, Lindenmeyer, Maja, Reichelt, Robert M., Beck, Sebastian, Politis, Panagiotis, Charonis, Aristidis, Kretz, Markus, Huber, Tobias B., Liu, Shuya, Banas, Bernhard and Banas, Miriam C. (2019) Glomerular expression pattern of long non-coding RNAs in the type 2 diabetes mellitus BTBR mouse model. Scientific Reports 9 (1). Fulltext not available.

Zakrzewska, Sandra, Mehdipour, Ahmad Reza , Malviya, Viveka Nand, Nonaka, Tsuyoshi, Koepke, Juergen, Muenke, Cornelia, Hausner, Winfried, Hummer, Gerhard , Safarian, Schara and Michel, Hartmut (2019) Inward-facing conformation of a multidrug resistance MATE family transporter. Proceedings of the National Academy of Sciences 116 (25), pp. 12275-12284. Fulltext not available.

Jakob, Leonhard, Gust, Alexander and Grohmann, Dina (2018) Evaluation and optimisation of unnatural amino acid incorporation and bioorthogonal bioconjugation for site-specific fluorescent labelling of proteins expressed in mammalian cells. Biochemistry and Biophysics Reports 2019 (17), pp. 1-9.

Dexl, Stefan Albin, Reichelt, Robert, Kraatz, Katharina, Schulz, Sarah, Grohmann, Dina, Bartlett, Michael and Thomm, Michael (2018) Displacement of the transcription factor B reader domain during transcription initiation. Nucleic Acids Research 46 (19), pp. 10066-10081.

Zander, Adrian (2018) Biochemische Charakterisierung des archäellen Argonaute-Proteins aus Methanocaldococcus jannaschii und strukturelle Untersuchungen mit Einzelmolekül-Förster-Resonanz-Energie-Transfer-Studien. PhD, Universität Regensburg.

Gust, Alexander, Jakob, Leonhard, Zeitler, Daniela M., Bruckmann, Astrid, Kramm, Kevin, Willkomm, Sarah, Tinnefeld, Philip, Meister, Gunter and Grohmann, Dina (2018) Site-Specific Labelling of Native Mammalian Proteins for Single-Molecule FRET Measurements. ChemBioChem 19 (8), pp. 780-783. Fulltext not available.

Eckl, Daniel B., Dengler, Linda, Nemmert, Marina, Eichner, Anja, Bäumler, Wolfgang and Huber, Harald (2017) A Closer Look at Dark Toxicity of the Photosensitizer TMPyP in Bacteria. Photochemistry and Photobiology 94 (1), pp. 165-172. Fulltext not available.

Heyam, Alex , Coupland, Claire E., Dégut, Clément, Haley, Ruth A., Baxter, Nicola J., Jakob, Leonhard, Aguiar, Pedro M. , Meister, Gunter, Williamson, Michael P., Lagos, Dimitris and Plevin, Michael J. (2017) Conserved asymmetry underpins homodimerization of Dicer-associated double-stranded RNA-binding proteins. Nucleic Acids Research 45 (21), pp. 12577-12584. Fulltext not available.

Zander, Adrian, Willkomm, Sarah, Ofer, Sapir, van Wolferen, Marleen, Egert, Luisa, Buchmeier, Sabine, Stöckl, Sarah, Tinnefeld, Philip, Schneider, Sabine , Klingl, Andreas, Albers, Sonja-Verena, Werner, Finn and Grohmann, Dina (2017) Guide-independent DNA cleavage by archaeal Argonaute from Methanocaldococcus jannaschii. Nature Microbiology 2 (6). Fulltext not available.

Beblo-Vranesevic, Kristina, Galinski, Erwin A., Rachel, Reinhard, Huber, Harald and Rettberg, Petra (2017) Influence of osmotic stress on desiccation and irradiation tolerance of (hyper)-thermophilic microorganisms. Archives of Microbiology 199 (1), pp. 17-28. Fulltext not available.

Gouge, Jerome , Guthertz, Nicolas, Kramm, Kevin, Dergai, Oleksandr, Abascal-Palacios, Guillermo, Satia, Karishma, Cousin, Pascal, Hernandez, Nouria, Grohmann, Dina and Vannini, Alessandro (2017) Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation. Nature Communications 8 (1). Fulltext not available.

Kucher, Svetlana, Korneev, Sergei, Tyagi, Swati, Apfelbaum, Ronja , Grohmann, Dina, Lemke, Edward A. , Klare, Johann P. , Steinhoff, Heinz-Jürgen and Klose, Daniel (2017) Orthogonal spin labeling using click chemistry for in vitro and in vivo applications. Journal of Magnetic Resonance 275, pp. 38-45. Fulltext not available.

Willkomm, Sarah, Oellig, Christine A., Zander, Adrian, Restle, Tobias, Keegan, Ronan, Grohmann, Dina and Schneider, Sabine (2017) Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein. Nature Microbiology 2 (6). Fulltext not available.

Yuan, Y. Adam, Willkomm, Sarah, Zander, Adrian, Grohmann, Dina and Restle, Tobias (2016) Mechanistic Insights into Archaeal and Human Argonaute Substrate Binding and Cleavage Properties. PLOS ONE 11 (10), e0164695. Fulltext not available.

Sheppard, Carol , Blombach, Fabian , Belsom, Adam, Schulz, Sarah, Daviter, Tina, Smollett, Katherine, Mahieu, Emilie, Erdmann, Susanne , Tinnefeld, Philip, Garrett, Roger, Grohmann, Dina, Rappsilber, Juri and Werner, Finn (2016) Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP. Nature Communications 7 (1). Fulltext not available.

Jakob, Leonhard, Treiber, Thomas, Treiber, Nora, Gust, Alexander, Kramm, Kevin, Hansen, Kerrin, Stotz, Mathias, Wankerl, Ludwig, Herzog, Franz, Hannus, Stefan, Grohmann, Dina and Meister, Gunter (2016) Structural and functional insights into the fly microRNA biogenesis factor Loquacious. RNA 22 (3), pp. 383-396. Fulltext not available.

Schulz, Sarah, Gietl, Andreas, Smollett, Katherine , Tinnefeld, Philip, Werner, Finn and Grohmann, Dina (2016) TFE and Spt4/5 open and close the RNA polymerase clamp during the transcription cycle. Proceedings of the National Academy of Sciences 113 (13), E1816-E1825. Fulltext not available.

Lobasso, Simona, Lopalco, Patrizia , Angelini, Roberto , Vitale, Rita , Huber, Harald, Müller, Volker and Corcelli, Angela (2012) Coupled TLC and MALDI-TOF/MS Analyses of the Lipid Extract of the Hyperthermophilic ArchaeonPyrococcus furiosus. Archaea 2012, pp. 1-10. Fulltext not available.

Anderson, Iain J., Sun, Hui, Lapidus, Alla , Copeland, Alex, Glavina Del Rio, Tijana, Tice, Hope, Dalin, Eileen, Lucas, Susan, Barry, Kerrie , Land, Miriam , Richardson, Paul, Huber, Harald and Kyrpides, Nikos C. (2009) Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1. Standards in Genomic Sciences 1 (2), pp. 183-188. Fulltext not available.

Ouhammouch, Mohamed, Hausner, Winfried and Geiduschek, E. Peter (2009) TBP domain symmetry in basal and activated archaeal transcription. Molecular Microbiology 71 (1), pp. 123-131. Fulltext not available.

Lundgren, Magnus, Malandrin, Laurence, Eriksson, Stefan, Huber, Harald and Bernander, Rolf (2008) Cell Cycle Characteristics of Crenarchaeota : Unity among Diversity. Journal of Bacteriology 190 (15), pp. 5362-5367. Fulltext not available.

Sutter, Markus , Boehringer, Daniel, Gutmann, Sascha, Günther, Susanne, Prangishvili, David, Loessner, Martin J , Stetter, Karl O, Weber-Ban, Eilika and Ban, Nenad (2008) Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nature Structural & Molecular Biology 15 (9), pp. 939-947. Fulltext not available.

Kelly, Donovan P., Uchino, Yoshihito, Huber, Harald, Amils, Ricardo and Wood, Ann P. (2007) Reassessment of the phylogenetic relationships of Thiomonas cuprina. International Journal of Systematic and Evolutionary Microbiology 57 (11), pp. 2720-2724. Fulltext not available.

Rocha, Rita, Leal, Sónia S. , Teixeira, Vitor H. , Regalla, Manuela, Huber, Harald, Baptista, António M. , Soares, Cláudio M. and Gomes, Cláudio M. (2006) Natural Domain Design: Enhanced Thermal Stability of a Zinc-Lacking Ferredoxin Isoform Shows that a Hydrophobic Core Efficiently Replaces the Structural Metal Site. Biochemistry 45 (34), pp. 10376-10384. Fulltext not available.