GRK  2062 "Molecular Principles of Synthetic Biology"
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Publications

2019

Brameyer, S., Rösch, T.C., El Andari, J., Hoyer, E., Schwarz, J., Graumann, P.L., and Jung, K. (2019). DNA-binding directs the localization of a membrane-integrated receptor of the ToxR family. Commun Biol 2, 4.
https://doi.org/10.1038/s42003-018-0248-7

de Boer, M., Gouridis, G., Vietrov, R., Begg, S.L., Schuurman-Wolters, G.K., Husada, F., Eleftheriadis, N., Poolman, B., McDevitt, C.A., and Cordes, T. (2019). Conformational and dynamic plasticity in substrate-binding proteins underlies selective transport in ABC importers. eLife 8, e44652.
https://doi.org/10.7554/eLife.44652.001

Dupin, A., and Simmel, F.C. (2019). Signalling and differentiation in emulsion-based multi-compartmentalized in vitro gene circuits. Nat Chem 11, 32-39.
https://doi.org/10.1038/s41557-018-0174-9

Glock, P., Ramm, B., Heermann, T., Kretschmer, S., Schweizer, J., Mücksch, J., Alagöz, G., and Schwille, P. (2019). Stationary patterns in a two-protein reaction-diffusion system. ACS Synth Biol 2018.
https://doi.org/10.1021/acssynbio.8b00415

Hürtgen, D.*, Härtel, T.*, Murray, S.M., Sourjik, V., and Schwille, P. (* contributed equally) (2019). Functional modules of minimal cell division for synthetic biology. Adv Biosyst 2019, 1800315.
https://doi.org/10.1002/adbi.201800315

Jung, K., Brameyer, S., Fabiani, F., Gasperotti, A., and Hoyer, E. (2019). Phenotypic heterogeneity generated by histidine kinase-based signaling networks. J Mol Biol, Apr 7. pii: S0022-2836(19)30184-6. [Epub ahead of print]
https://doi.org/10.1016/j.jmb.2019.03.032

Scheidler, C.M., Kick, L.M., and Schneider, S. (2019). Ribosomal peptides and small proteins on the rise. ChemBioChem
https://doi.org/10.1002/cbic.201800715

Volkwein, W., Krafczyk, R., Jagtap, P.K.A., Parr, M., Mankina, E., Macošek, J., Guo, Z.,Fürst, M.J., Pfab, M., Frishman, D., Hennig, J., Jung, K., and Lassak, J. (2019). Switching the post-translational modification of translation elongation factor EF P. Frontiers in Microbiology, section Microbial Physiology and Metabolism, accepted. https://doi.org/10.3389/fmicb.2019.01148

2018

Baumann, A., Marchner, S., Daum, M., and Hoffmann-Röder, A. (2018). Synthesis of fluorinated Leishmania cap trisaccharides for diagnostic tool and vaccine development. Eur J Org Chem 2018, 3803-3815.
https://doi.org/10.1002/ejoc.201800384

Carell, T., Kurz, M.Q., Müller, M., Rossa, M., and Spada, F. (2018). Non-canonical bases in the genome: the regulatory information layer in DNA. Angew Chem Int Ed Engl 57, 4296–4312.
https://doi.org/10.1002/anie.201708228

Glock, P., Broichhagen, J., Kretschmer, S., Blumhardt, P., Mücksch, J., Trauner, D., and Schwille, P. (2018). Optical control of a biological reaction-diffusion system. Angew Chem Int Ed Engl 57, 2362–2366. 
https://doi.org/10.1002/anie.201712002

Glock, P. and Schwille, P. (2018). Switching protein patterns on membranes. Curr Opin Colloid Interface Sci 38, 100–107.
https://doi.org/10.1016/j.cocis.2018.10.004

Halatek, J., Brauns, F., and Frey, E. (2018). Self-organisation principles of intracellular pattern formation. Phil Trans R Soc B 373, 20170107.
https://doi.org/10.1098/rstb.2017-0107

Herzog, R., and Papenfort, K. (2018) Chapter thirteen - Transcriptomic approaches for studying quorum sensing in Vibrio cholerae. In: Methods in Enzymology 612, 303-342.
https://doi.org/10.1016/bs.mie.2018.09.008

Jia, H., Kai, L., Heymann, M., García-Soriano, D.A., Härtel, T., and Schwille, P. (2018). Light-induced printing of protein structures on membranes in vitro. Nano Lett 18, 7133-7140.
https://doi.org/10.1021/acs.nanolett.8b03187

Jung, K., Fabiani, F., Hoyer, E., and Lassak, J. (2018). Bacterial transmembrane signalling systems and their engineering for biosensing. Open Biol 8, 180023.
https://doi.org/10.1098/rsob.180023

Leister, D. (2018). Genetic engineering, synthetic biology and the light reactions of photosynthesis. Plant Physiol, pp.00360.02018.
https://doi.org/10.1104/pp.18.00360

Leister, D. (2018). Thawing out frozen metabolic accidents. BMC Biol, in press.

Lerner, E., Cordes, T., Ingargiola, A., Alhadid, Y., Chung, S., Michalet, X., and Weiss, S. (2018). Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science Vol. 359, Issue 6373
https://doi.org/10.1126/science.aan1133

Litschel, T., Ganzinger, K., Movinkel, T., Heymann, M., Robinson, T., Mutschler, H., and Schwille, P. (2018). Optimizing content mixing of protocell models in freeze-thaw cycles. New J Phys 20, 055008.
https://doi.org/10.1088/1367-2630/aabb96

Litschel, T., Ramm, B., Mass, R., Heymann, M., and Schwille, P. (2018). Beating vesicles: Encapsulated protein oscillations cause dynamic membrane deformations. Angew Chem Int Ed 57, 16286-16290.
https://doi.org/10.1002/anie.201808750

Miermans, C.A., and Broedersz, C.P. (2018). Bacterial chromosome organization by collective dynamics of SMC condensins. J Royal Soc Interface 15, 20180495.
https://doi.org/10.1098/rsif.2018.0495

Mückl, A., Schwarz-Schilling, M., Fischer, K., and Simmel, F.C. (2018). Filamentation and restoration of normal growth in Escherichia coli using a combined CRISPRi sgRNA/antisense RNA approach. PLoS One 13, e0198058.
https://doi.org/10.1371/journal.pone.0198058

Niederauer, C., Blumhardt, P., Mücksch, J., Heymann, M., Lambacher, A., and Schwille P., (2018). Direct characterization of the evanescent field in objective-type total internal reflection microscopy. Opt Express 26, 20492-20506.
https://doi.org/10.1364/OE.26.020492

Pardatscher, G.*, Schwarz-Schilling, M.*, Sagredo, S., and Simmel, F.C. (2018). Functional surface-immobilization of genes using multistep strand displacement lithography. *Shared authorship. J Vis Exp, accepted. https://www.jove.com/video/58634/functional-surface-immobilization-genes-using-multistep-strand

Pardatscher, G., Schwarz-Schilling, M., Daube, S.S., Bar-Ziv, R.H., and Simmel, F.C. (2018). Gene expression on DNA biochips patterned with strand-displacement lithography. Angew Chem Int Ed 57, 4783-4786
https://doi.org/10.1002/anie.201800281

Ramm B, Glock P, and Schwille P. (2018). In vitro reconstitution of self-organizing protein patterns on supported lipid bilayers. J Vis Exp 137, e58139.
https://www.jove.com/video/58139/in-vitro-reconstitution-self-organizing-protein-patterns-on-supported

Ramm, B., Glock, P., Mücksch, J., Blumhardt, P., Heymann, M., and Schwille, P. (2018). The MinDE system is a generic spatial cue for membrane protein distribution in vitro. Nat Commun 9, 3942.
https://www.nature.com/articles/s41467-018-06310-1

Schiefner, A., Nästle, L., Landgraf, M., Reichert, A. J., and Skerra, A. (2018). Structural basis for the specific cotranslational incorporation of p-boronophenylalanine into biosynthetic proteins. Biochemistry 57, 2597-2600.
https://doi.org/10.1021/acs.biochem.8b00171

Schwarz-Schilling, M., Dupin, A., Chizzolini, F., Krishnan, S., Mansy, S.S., and Simmel, F.C. (2018). Optimized assembly of a multifunctional RNA-protein nanostructure in a cell-free gene expression system. Nano Lett 18, 2650-2657.
https://doi.org/10.1021/acs.nanolett.8b00526

Wilke, P., Reithmann, E., and Frey, E. (2018). Two-species active transport along cylindrical biofilaments is limited by emergent topological hindrance. Phys Rev X 8, 031063.
https://doi.org/10.1103/PhysRevX.8.031063

2017

Dann, M., and Leister, D. (2017). Enhancing (crop) plant photosynthesis by introducing novel genetic diversity. Phil Trans R Soc B 372, 20160380.
http://doi.org/10.1098/rstb.2016.0380

Edupuganti, R.R., Geiger, S., Lindeboom, R.G.H., Shi, H., Hsu, P.J., Lu, Z., Wang, S.-Y., Baltissen, M.P.A., Jansen, P.W.T.C., Rossa, M., Müller, M., Stunnenberg, H. G., He, C., Carell, T., and Vermeulen, M. (2017). N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis. Nat Struct Mol Biol 24, 870–878.

Edwardraja, S., Eichinger, A., Theobald, I., Sommer, C.A., Reichert, A.J., and Skerra, A. (2017). Rational design of an anticalin-type sugar-binding protein using a genetically encoded boronate side chain. ACS Synth Biol 6, 2241-2247.
https://doi.org/10.1021/acssynbio.7b00199

Gandini, C., Schmidt, S.B., Husted, S., Schneider, A., and Leister, D. (2017). The transporter SynPAM71 is located in the plasma membrane and thylakoids, and mediates manganese tolerance in Synechocystis PCC6803. New Phytol 215, 256-268.
http://dx.doi.org/10.1111/nph.14526

Gladrow, J., Broedersz, C.P., and Schmidt, C.F. (2017) Nonequilibrium dynamics of probe filaments in actin-myosin networks. Physical  Review E 96, 022408
http://dx.doi.org/10.1103/PhysRevE.96.022408

Jia, H., Heymann, M., Bernhard, F., Schwille, P., and Kai, L. (2017). Cell-free protein synthesis in micro compartments: building a minimal cell from biobricks. New Biotechnol 39, 199-205.
https://doi.org/10.1016/j.nbt.2017.06.014

Kick, L., Kirchner, M., and Schneider, S. (2017). CRISPR-Cas9: from a bacterial immune system to genome-edited human cells in clinical trials. Bioengineered 8, 280-286.
https://doi.org/10.1080/21655979.2017.1299834

Kirchner, M., and Schneider, S. (2017). Gene expression control by Bacillus anthracis purine riboswitches. RNA 23, 762-9.
http://dx.doi.org/10.1261/rna.058792.116

Kirchner, M., Schorpp, K., Hadian, K., and Schneider, S. (2017). An in vivo high-throughput screening for riboswitch ligands using a reverse reporter gene system. Sci Rep 7, 7732.
http://doi.org/10.1038/s41598-017-07870-w

Kitsera, N., Allgayer, J., Parsa, E., Geier, N., Rossa, M., Carell, T., and Khobta, A. (2017). Functional impacts of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine at a single hemi-modified CpG dinucleotide in a gene promoter. Nucleic Acids Res 45, 11033–11042.
https://doi.org/10.1093/nar/gkx718

Krafczyk, R., Macošek, J., Jagtap, P.K.A., Gast, D., Wunder, S., Mitra, P., Jha, A.K., Rohr, J., Hoffmann-Röder, A., Jung, K., Hennig, J., and Lassak, J. (2017). Structural basis for EarP-mediated arginine glycosylation of translation elongation factor EF-P. mBio 8, e01412-17.
https://doi.org/10.1128/mBio.01412-17

Leister, D. (2017) Experimental evolution in photoautotrophic microorganisms as a means of enhancing chloroplast functions. Essays in Biochem 2017 Sep 7
https://doi.org/10.1042/EBC20170010

Paieri, F., Tadini, L., Manavski, N., Kleine, T., Morandini, P., Pesaresi, P., Meurer, J., and Leister, D. (2017). The DEAD-box RNA helicase RH50 is a 23S-4.5S rRNA maturation factor that functionally overlaps with the plastid signaling factor GUN1. Plant Physiol 176, 634–648.
https://doi.org/10.1104/pp.17.01545

Volkwein, W., Maier, C., Krafczyk, R., Jung, K., and Lassak, J. (2017). A versatile toolbox for the control of protein levels using Nε-acetyl-L-lysine dependent amber suppression, ACS Synth Biol 6, 1892-1902.
http://dx.doi.org/10.1021/acssynbio.7b00048

Wang, Y., Heermann. R., and Jung, J. (2017) CipA and CipB as scaffolds to organize proteins into crystalline inclusions. ACS Synthetic Biology
http://dx.doi.org/10.1021/acssynbio.6b00323

2016

Fröhlich, K.S., and Papenfort, K. (2016).  Interplay of regulatory RNAs and mobile genetic elements in enteric pathogens. Mol Microbiol
http://dx.doi.org/10.1111/mmi.13428

Fröhlich, K.S., Haneke, K., Papenfort, K., and Vogel, J. (2016). The target spectrum of SdsR small RNA in Salmonella.  Nucl Acids Res
http://dx.doi.org/10.1093/nar/gkw632

Li, X., Krafczyk, R., Macoşek, J., Li, Y.-L., Zou, Y., Simon, B., Pan, X., Wu, Q.-Y., Yan, F, Li, S., Hennig, J., Jung, K., Lassak, J., and Hu, H.-G. (2016). Resolving the α-glycosidic linkage of arginine-rhamnosylated translation elongation factor P (EF-P) triggers generation of the first ArgRha specific antibody. Chem Sci 7, 6995-7001.
http://dx.doi.org/10.1039/C6SC02889F 

Schwarz-Schilling, M., Aufinger, L., Muckl, A., and Simmel, F.C. (2016). Chemical communication between bacteria and cell-free gene expression systems within linear chains of emulsion droplets. Integr Biol 8, 564-570.
http://dx.doi.org/10.1039/C5IB00301F

Schwarz-Schilling, M., Kim, J., Cuba, C., Weitz, M., Franco, E., and Simmel, F.C. (2016). Building a synthetic transcriptional oscillator. Methods Mol Biol 1342, 185-99.
http://dx.doi.org/10.1007/978-1-4939-2957-3_10

Wunder, S., Deutsch, A., Deutsch, C., and Hoffmann-Röder, A. (2016). One-pot synthesis of functionalized β-fluoroalkylated Mannich-type products from N-aryl N,O-acetals. Synthesis 48, 1167-1176.
https://doi.org/10.1055/s-0035-1561324

2015

Kirchner, M., and Schneider, S. (2015). CRISPR - Cas: From the bacterial adaptive immune system to a versatile genome engineering toolbox. Angew Chem Int Ed 54, 13508-13514.
http://dx.doi.org/10.1002/anie.201504741

Reichert, A.J., Poxleitner, G., Dauner, M. and Skerra, A. (2015). Optimisation of a system for the co-translational incorporation of a keto amino acid and its application to a tumour-specific Anticalin. Protein Eng Des Sel 28, 553-565.
http://dx.doi.org/10.1093/protein/gzv048


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