Publications

Helmbrecht V, Reichelt R, Grohmann D, Orsi WD. Simulated early Earth geochemistry fuels a hydrogen-dependent primordial metabolism.
Nat Ecol Evol. 2025 May;9(5):769-778. doi: 10.1038/s41559-025-02676-w. Epub 2025 Apr 30.

Grohmann D, Grünberger F. Single-molecule sequencing of RNA.
American Chemical Society. 2025 April 24; DOI: 10.1021/acsinfocus.7e9002

Hanelt TN, Treiber N, Treiber T, Lehmann G, Eichner N, Rothmeier T, Schmid G, Reichelt R, Zambelli F, Pavesi G, Grohmann D, Meister G. Endo-bind-n-seq: identifying RNA motifs of RNA binding proteins isolated from endogenous sources.
Life Sci Alliance. 2024 Dec 2;8(2):e202402782. doi: 10.26508/lsa.202402782

Tarau D, Grünberger F, Pilsl M, Reichelt R, Hei? F, K?nig S, Urlaub H, Hausner W, Engel C, Grohmann D. Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment.
Nucleic Acids Research, gkae282, https://doi.org/10.1093/nar/gkae282

2022

Kaul A., B?llmann A., Thema M., Kalb L., St?ckl R., Huber H., Sterner M., Bellack A. (2022). Combining a robust thermophilic methanogen and packing material with high liquid hold-up to optimize biological methanation in trickle-bed reactors. Bioresource Technology 345:126524. DOI: 10.1016/j.biortech.2021.126524

Dengler L, Meier J, Grünberger F, Bellack A, Rachel R, Grohmann D, Huber H. Methanofollis propanolicus sp. nov., a novel archaeal isolate from a Costa Rican oil well that uses propanol for methane production. Arch Microbiol. 2022 Aug 13;204(9):554.
doi: 10.1007/s00203-022-03152-w

Gambelli L., Isupov M. N., Conners R., McLaren M., Bellack A., Gold V., Rachel R., Daum B. (2022). An archaellum filament composed of two alternating subunits. Nature Communications 13:710. DOI: 10.1038/s41467-022-28337-1

Willkomm S., Jakob L., Kramm K., Graus V., Neumeier J., Meister G., Grohmann D. (2022).?Single-molecule FRET uncovers hidden conformations and dynamics of human Argonaute 2. Nat Commun 13, 3825.?https://doi.org/10.1038/s41467-022-31480-4

Buriánková, I.; Molíková, A.; Vítězová, M.; Onderka, V.; Vítěz, T.; Urbanová, I.; Hani?áková, N.; ?ern?, M.; Novák, D.; Lochman, J.; Zeman, J.; Jav?rek, J.; Machálková, M.; Dengler, L.; Huber, H. (2022). Microbial Communities in Underground Gas Reservoirs Offer Promising Biotechnological Potential. Fermentation 2022, 8, 251. https://doi.org/10.3390/fermentation8060251

S. H?llerer, M. Jeschek. (2022). Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript. bioRxiv doi: https://doi.org/10.1101/2022.05.02.490318

W?rle E, Newman A, D'Silva J, Burgio G, Grohmann D. Allosteric activation of CRISPR-Cas12a requires the concerted movement of the bridge helix and helix 1 of the RuvC II domain. Nucleic Acids Res. 2022 Sep 23;50(17):10153-10168.
doi:10.1093/nar/gkac767

Grünberger F., Ferreira-Cerca S. and Grohmann D. (2022) Nanopore sequencing of RNA and cDna molecules in Escherichia coli. RNA 28(3): 400-417.
doi:?10.1261/rna.078937.121

2021

2020

Eder W., Tindall B. J., Huber H., Peplies J., Wirth R. (2020). Recognition of the unsuitability of DSM 12173 as the deposited type strain of Thermocrinis ruber Huber et al. 1999, recognition of DSM 23557 as an authentic sub?culture of strain OC 1/4, the nomenclatural type of Thermocrinis ruber Huber et al. 1999 and an emended description of Thermocrinis ruber Huber et al. 1999. Archives of Microbiology. DOI: 10.1007/s00203-020-01850-x.

Eckl D. B., Huber H., B?umler W. (2020). First report on Photodynamic Inactivation of Archaea including a novel method for high-throughput reduction measurement. Photochemistry and Photobiology. DOI: 10.1111/php.13229.

Rose S., Auxilien S., Havelund J. F., Kirpekar F., Huber H., Grosjean H., Douthwaite S. (2020). The hyperthermophilic partners Nanoarchaeum and Ignicoccus stabilize their tRNA T-loops via different but structurally equivalent modifications. Nucleic acids research. DOI: 10.1093/nar/gkaa411.

2019

S. Wu, Y. Zhou, D. Gerngross, M. Jeschek, T.R. Ward. (2019) Chemo-enzymatic cascades to produce cycloalkenes from bio-based resources. Nature Communications 10:5060. https://www.nature.com/articles/s41467-019-13071-y

Kramm K., Endesfelder U., Grohmann D. (2019). A single-molecule view of archaeal transcription. Journal of Molecular Biology. DOI: 10.1016/j.jmb.2019.06.009.

Grünberger F., Reichelt R.M., Bunk B., Spr?er C., Overmann J., Rachel R., Grohmann D., Hausner W. (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 10, 1603. DOI: 10.3389/fmicb.2019.01603.

Kramm K., Engel C., Grohmann D. (2019) Transcription factor TBP: Old friend new questions. Biochem Soc Trans. 47: 411 – 423. DOI: 10.1042/BST20180623.

Jakob L., Gust A., Grohmann D. (2019) 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 17, 1-9. DOI: 10.1016/j.bbrep.2018.10.011.

Kreuter L. J., Weinfurtner A., Ziegler A., Weigl J., Hoffmann J., Morgner N. , Müller V., Huber H. (2019). Purification of a crenarchaeal ATP synthase in the light of the unique bioenergetics of Ignicoccus species. J. Bacteriol. Vol 201, e00510-18; DOI: 10.1128/JB.00510-18.

Thema M., Weidlich T., H?rl M., Bellack A., M?rs F., Hackl F., Kohlmayer M., Gleich J., Stabenau C., Trabold T., Neubert M., Ortlo F., Brotsack R., Schmack D., Huber H.,? Hafenbradl D., Karl J., Sterner M. (2019). Biological CO2-Methanation: An Approach to Standardization. Energies 12, 1670; DOI: 10.3390/en12091670.

2018

T. Heinisch, F. Schwizer, B. Garabedian, E. Csibra, M. Jeschek, J. Vallapurackal, V.B. Pinheiro, P. Marlière, S. Panke, T.R. Ward. (2018). E. coli surface display of streptavidin for directed evolution of an allylic deallylase. Chemical Science 9:5383–5388. https://pubs.rsc.org/en/content/articlelanding/2018/sc/c8sc00484f

M. Jeschek, S. Panke, T.R. Ward. (2018) Artificial metalloenzymes on the verge of new-to-nature metabolism. Trends in Biotechnology 36:60-72. https://pubs.rsc.org/en/content/articlelanding/2018/sc/c8sc00484f

Reichelt R., Grohmann D., Willkomm S. (2018) A journey through the evolutionary diversification of archaeal Lsm and Hfq proteins. Emerging topics in life sciences. 2: 647-657. DOI: 10.1042/ETLS20180034.

Dexl S., Reichelt R., Kraatz K., Schulz S., Grohmann D., Bartlett M., Thomm M. (2018) Displacement of the Transcription Factor B Reader Domain during Transcription Initiation. Nucleic Acids Research. 46: 10066 – 10081. DOI: 10.1093/nar/gky699.

Molle J., Jakob L., Bohlen J., Raab M., Tinnefeld P., Grohmann D. (2018) Towards Structural Biology with Super-Resolution Microscopy. Nanoscale. 10: 16416 – 16424. DOI: 10.1039/c8nr03361g.

Willkomm S., Makaraova K. and Grohmann D., (2018) Prokaryotic Argonaute proteins represent an additional layer in prokaryotic defence. FEMS Microbiology Reviews. 42:376-387. DOI: 10.1093/femsre/fuy010.

Gust A., Jakob L., Zeitler D., Willkomm S., Kramm K., Tinnefeld P., Meister G. and Grohmann D. (2018) Site-specific fluorescent labelling of endogenous mammalian proteins for single-molecule FRET analysis. ChemBioChem. 19:780-783. DOI: 10.1002/cbic.201700696.

2017

M. Jeschek, M.O. Bahls, V. Schneider, P. Marlière, T.R. Ward, S. Panke. (2017). Biotin-independent strains of Escherichia coli for enhanced streptavidin production. Metabolic Engineering 40:33-40. https://pubmed.ncbi.nlm.nih.gov/28062280/

Gouge J., Guthertz N., Dergai O., Kramm K., Abascal-Palacios G., Satia K., Cousin P., Nouria Hernandez N., Grohmann D. and Vannini A. (2017). Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA Polymerase III transcription initiation. Nature Structural and Molecular Biology, Nature Communications. 8(1): 130. DOI: 10.1038/s41467-017-00126-1.

M. Jeschek, D. Gerngross, S. Panke. (2017) Combinatorial pathway optimization for streamlined metabolic engineering. Current Opinion in Biotechnology 47:142-151. https://pubmed.ncbi.nlm.nih.gov/28750202/

Blombach F. and Grohmann D. (2017). Same same but different: the evolution of TBP in archaea and their eukaryotic offspring. Transcription. 8:162-168. DOI: 10.1080/21541264.2017.1289879.

Willkomm S., Zander A. and Grohmann D. (2017). Site-Specific Fluorescent Labeling of Argonaute for FRET-based Bio-Assays. Methods in Molecular Biology, 1517:291-304. DOI: 10.1007/978-1-4939-6563-2_20.

Zander A., Willkomm S., Ofer S., van Wolferen M., Egert L., Buchmeier S., St?ckl S., Tinnefeld P., Schneider S., Klingl A., Albers S.-V., Werner F. and Grohmann D. (2016). Guide-independent DNA silencing by archaeal Argonaute. Nature Microbiology. 2: 17034. DOI: 10.1038/nmicrobiol.2017.35.

Willkomm S, Oellig C. A., Zander A., Restle T., Keegan R., Grohmann D.* and Schneider, S. (2016). Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein. Nature Microbiology. 2:17035. DOI: 10.1038/nmicrobiol.2017.35.

Kucher S, Korneev S. Tyagi S., Apfelbaum R., Grohmann D., Lemke E.A., Klare, J., Steinhoff H.-J., Klose, D. (2016) Orthogonal spin labelling using click chemistry for in vitro and in vivo applications. Journal of Magnetic Resonance, 275:38-45. DOI: 10.1016/j.jmr.2016.12.001.

2016

M. Jeschek, S. Panke, T. R. Ward. (2016). Periplasmic screening for artificial metalloenzymes. Methods in Enzymology 580:539-556. https://pubmed.ncbi.nlm.nih.gov/27586348/

M. Jeschek, R. Reuter, T. Heinisch, C. Trindler, J. Klehr, S. Panke, T.R. Ward. (2016). Directed evolution of artificial metalloenzymes for in vivo metathesis. Nature 537:661-665. https://www.nature.com/articles/nature19114

M. Jeschek, D. Gerngross, S. Panke. (2016) Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort. Nature Communications 7:11163. https://www.nature.com/articles/ncomms11163

Sheppard C., Blombach F., Belsom A., Schulz S., Daviter T., Smollett K., Mahieu E., Erdmann S., Tinnefeld P., Garrett R., Grohmann D., Rappsilber J., Werner F. (2016) Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP. Nature Communications, 7:13595. DOI: 10.1038/ncomms13595.

Nickels P.C., Wünsch B., Holzmeister P., Bae W., Kneer L.M., Grohmann D., Tinnefeld P. and Liedl T. (2016), Molecular Force Spectroscopy with a DNA Origami-Based Nanoscopic Force Clamp. Science. 354(6310):305-307. DOI: 10.1126/science.aah5974.

Willkomm S., Zander A., Grohmann D. and Restle T. (2016). Mechanistic insights into archaeal and human Argonaute substrate binding and cleavage properties. PLOS one, 11(10):e0164695. DOI: 10.1371/journal.pone.0164695.

Blombach B., Smollett K.L., Grohmann D. and Werner F. (2016). Molecular Mechanisms of Transcription Initiation – structure, function and evolution of TFE/TFIIE-like factors and open complex formation. Journal of Molecular Biology (epub, ahead of print). DOI: 10.1016/j.jmb.2016.04.016.

Schulz S., Gietl A., Smollett K., Tinnefeld P., Werner F. and Grohmann D. (2016). TFE and Spt4/5 open and close the RNA polymerase clamp during the transcription cycle. PNAS (epub, ahead of print) Selected by the Faculty 1000

Jakob L., Treiber T., Treiber N., Gust A., Kramm K., Hansen K., Stotz M., Wankerl L., Herzog F., Hannus S., Grohmann D., and Meister G. (2016). Structural and functional insights into the fly microRNA biogenesis factor Loquacious. RNA. (epub ahead of print). DOI: 10.1261/rna.055426.115.

Molle J., Raab M., Holzmeister S., Schmitt-Monreal D., Grohmann D., He Z., Tinnefeld P. (2016). Superresolution microscopy with transient binding. Current Opinion in Biotechnology, 39: 8-16. DOI: 10.1016/j.copbio.2015.12.009.

2015

Schulz S., Kramm K., Werner F., Grohmann D. (2015). A fluorescently labeled recombinant RNAP system to probe archaeal transcription initiation. Methods (epub, ehead of print). DOI: 10.1016/j.ymeth.2015.04.017.

Willkomm S., Zander A., Gust A., Grohmann D. (2015). A prokaryotic twist on Argonaute action. Life. 5 (1), 538-553. DOI: 10.3390/life5010538.

Nagy J., Grohmann D., Cheung A.C.M., Schulz S., Smollett K., Werner F. & Michaelis J. (2015): Complete architecture of the archaeal RNA polymerase open complex from single-molecule FRET and NPS. Nature Communications, 6:6161. DOI: 10.1038/ncomms7161.

2014

A. Gust, A. Zander, A. Gietl, P. Holzmeister, S. Schulz, B. Lalkens, P. Tinnefeld, D. Grohmann (2014): A Starting Point for Fluorescence-Based Single-Molecule Measurements in Biomolecular Research. Molecules, 19, 10, 15824-15865. DOI: 10.3390/molecules191015824.

Acuna G., Grohmann D., Tinnefeld P. (2014) Enhancing single-molecule fluorescence with nanophotonics. FEBS letters. DOI: 10.1016/j.febslet.2014.06.016

Gietl A., Holzmeister P., Blombach F., Schulz S., Voithenberg L.V.v., Lamb D., Werner F., Tinnefeld P., Grohmann D. (2014) Eukaryotic and Archaeal TBP and TFB/TF(II)B Follow Different Promoter DNA Bending Pathways. Nucleic Acids Research. 42(10):6219-31. Selected by the Faculty 1000. DOI: 10.1093/nar/gku273.

Zander A., Holzmeister P., Klose D., Tinnefeld P. and Grohmann D. (2014). Single-molecule FRET supports the two-state model of Argonaute action. RNA Biology 11(1):45-56. (featured image from our article). DOI: 10.4161/rna.27446.

Afanasyeva A., Hirtreiter A., Schreiber A., Grohmann D., Pobegalov E., McKay A.R., Tsaneva I., Petukhov M., K?s E., Grigoriev M. and Werner F. (2014). Lytic water dynamics reveal evolutionarily conserved mechanisms of ATP hydrolysis by TIP49 AAA+ ATPases. Structure. 22(4):549-59. DOI: 10.1016/j.str.2014.02.002.

Holzmeister P., Acuna G.P., Grohmann D. and Tinnefeld P. (2014) Breaking the Concentration Limit of Optical Single-Molecule Detection. Chemical Society Reviews 43(4):1014-28. (back cover). DOI: 10.1039/C3CS60207A.

2013

Grohmann D.*, Werner F. and Tinnefeld P. (2013). Making Connections – Strategies for Single Molecule Fluorescence Biophysics. Current Opinion in Chemical Biology. 17(4):691-8. DOI: 10.1016/j.cbpa.2013.05.020.

Gietl A. and Grohmann D. (2012). Modern biophysical approaches probe transcription factor induced DNA bending and looping. Biochem Soc Trans. 41(1):368-73. DOI: 10.1042/BST20120301.

2012

Blombach F., Daviter T., Fielden D., Grohmann D., Smollett K. and Werner F. (2012). Archaeology of RNA polymerase – factor swapping during the transcription cycle. Biochem Soc Trans. 41(1):362-7. DOI: 10.1038/nmicrobiol.2017.21.

Klose D., Klare J., Grohmann D., Kay C.W.M., Werner F. and Steinhoff H-J. (2012). Simulation vs. reality: a comparison of in silico predictions with DEER and FRET measurements. PLOS one, 7(6):e39492. DOI: 10.1371/journal.pone.0039492.

Gietl A., Holzmeister P., Grohmann D.* and Tinnefeld P. (2012). DNA origami as biocompatible surface to match single-molecule and ensemble experiments. Nucleic Acids Research, epub. DOI: DOI: 10.1093/nar/gks326.

2011

Grohmann D., Nagy J., Chakraborty A., Klose D., Fielden D., Ebright R.H., Michaelis J., Werner F. (2011). The Initiation Factor TFE and the Elongation Factor Spt4/5 Compete for the RNAP Clamp during Transcription Initiation and Elongation. Molecular Cell, 43:263-74. DOI: 10.1016/j.molcel.2011.05.030.

Grohmann D. and Werner F. (2011) Recent advances in the understanding of archaeal transcription. Curr Opin Microbiol. DOI: 10.1016/j.mib.2011.04.012.

Ryan C.P., Smith M.E., Schumacher F.F., Grohmann D., Papaioannou D., Waksman G., Werner F., Baker J.R., Caddick S. (2011) Tunable reagents for multi-functional bioconjugation: reversible or permanent chemical modification of proteins and peptides by control of maleimide hydrolysis. Chem Commun. 47:5452-4. DOI: 10.1039/c1cc11114k.

Grohmann D., Klose D., Fielden D., Werner F. (2011) FRET (fluorescence resonance energy transfer) sheds light on transcription. Biochem Soc Trans. 39:122-7. DOI: 10.1042/BST0390122.

Werner F. and Grohmann D. (2011) Evolution of multisubunit RNA polymerases in the three domains of life. Nature Reviews Microbiol.9:85-98. DOI: 10.1038/nrmicro2507.

Grohmann D. and Werner F. (2011) Cycling through Transcription with the RNA polymerase F/E (RPB4/7) Complex - Structure, Function and Evolution of Archaeal RNA polymerase. Research in Microbiology 162:10-8. DOI: 10.1016/j.resmic.2010.09.002.

2010

Grohmann D., Klose D., Klare J.P., Kay C.W., Steinhoff H.J., Werner F. (2010) RNA-binding to archaeal RNA polymerase subunits F/E: a DEER and FRET study. J Am Chem Soc., 132:5954-5. DOI: 10.1021/ja101663d.

Hirtreiter A., Damsma G.E., Cheung A.C., Klose D., Grohmann D., Vojnic E., Martin A.C., Cramer P., Werner F. (2010). Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif. Nucleic Acids Research 38:4040-51. DOI: 10.1093/nar/gkq135.

Hirtreiter A., Grohmann D., Werner F. (2010) Molecular mechanisms of RNA polymerase – the F/E (Rpb4/7) complex is required for high processivity in vitro. Nucleic Acids Research, 38:585-96. DOI: 10.1093/nar/gkp928.

Grohmann, D. & Werner, F. (2010) Hold on!: RNA polymerase interactions with the nascent RNA modulate transcription elongation and termination. RNA Biology, 7: 310-315. DOI: 10.4161/rna.7.3.11912.

2009

Grohmann D., Hirtreiter A., Werner F. (2009). RNAP subunits F/E (Rpb4/7) are stably associated with archaeal RNA polymerase: using fluorescence anisotropy to monitor RNAP assembly in vitro. Biochem J, 421:339-43. (selected by the Faculty 1000). DOI: 10.1042/BJ20090782.

Grohmann D., Hirtreiter A., Werner F. (2009), Molecular mechanisms of archaeal RNA polymerase. Biochem Soc Trans. 37:12-7. DOI: 10.1042/BST0370012.

2008

Grohmann D., Godet J., Mely Y., Darlix JL. and Restle, T. (2008). HIV-1 NC traps the reverse transcriptase on primer/template substrates. Biochemistry, 47:12230-40. DOI: 10.1021/bi801386r.

Di Pasquale F, Fischer D, Grohmann D, Restle T, Geyer A, Marx A. (2008) Opposed steric constraints in human DNA polymerase beta and E.coli DNA polymerase I. J Am Chem Soc 130:10748-57. DOI: 10.1021/ja8028284.

Grohmann D., Corradi V., Horenkamp F., Laufer, S.D., Manetti, F. Botta, M. and Restle, T. (2008). Small molecule inhibitors targeting HIV-1 dimerization. Chembiochem 9:916-22. DOI: 10.1002/cbic.200700669.

2007

Yamazaki S., Tan L., Mayer G., Hartig J.S., Song J.N., Reuter S., Restle T., Laufer S.D., Grohmann D., Kr?usslich H.G., Bajorath J., Famulok M. (2007). Aptamer displacement identifies alternative small-molecule target sites that escape viral resistance. Chem Biol.14:804-12. DOI: 10.1016/j.chembiol.2007.06.003.

2006

Mescalchin A., Wünsche W., Laufer S.D., Grohmann, D., Restle, T. and Sczakiel, G. (2006). Specific binding of a bioactive hexanucleotide to HIV-1 reverse transcriptase: a novel class of small oligomeric nucleic acid drugs. Nucleic Acids Research, 34, 5631–5637. DOI: 10.1093/nar/gkl533.