Barone, G. D., Rodríguez-Seijo, A., Parati, M., Johnston, B., Erdem, E., Cernava, T., Zhu, Z., Liu, X., Axmann, I. M., Lindblad, P., & Radecka, I. (2024). Harnessing photosynthetic microorganisms for enhanced bioremediation of microplastics: A comprehensive review. Environmental Science and Ecotechnology, 100407. doi: 10.1016/j.ese.2024.100407
Becker, L., Spohr, P., Klau, G. W., Axmann, I. M., Fraune, S., & Schmelling, N. M. (2023). CATHI: An interactive platform for comparative genomics and homolog identification. In bioRxiv (p. 2023.09.04.556229). doi: 10.1101/2023.09.04.556229
Berwanger, L. C., Thumm, N., Gholamipoor, R., Wiegard, A., Schlebusch, J., Kollmann, M., & Axmann, I. M. (2023). Self-sustained rhythmic behavior of Synechocystis PCC 6803 under continuous light conditions in the absence of light-dark entrainment. In bioRxiv (p. 2023.09.26.559469). doi: 10.1101/2023.09.26.559469
Köbler, C., Schmelling, N. M., Pawlowski, A., Spät, P., Scheurer, N. M., Sebastian, K., Berwanger, L. C., Maček, B., Wiegard, A., Axmann, I. M., & Wilde, A. (2023). Two circadian oscillators in one cyanobacterium. In bioRxiv (p. 2021.07.20.453058). doi: 10.1101/2021.07.20.453058
Mager M, Pineda Hernandez H, Brandenburg F, López-Maury L, McCormick AJ, Nürnberg DJ, Orthwein T, Russo DA, Victoria AJ, Wang X, Zedler JAZ, Branco dos Santos F, Schmelling NM. Interlaboratory Reproducibility in Growth and Reporter Expression in the Cyanobacterium Synechocystis sp. PCC 6803. ACS Synthetic Biology 2023 12 (6), 1823-1835 doi: 10.1021/acssynbio.3c00150.
Germann, AT, Nakielski A, Dietsch M, Petzel T, Moser D, Triesch S, Westhoff P, Axmann IM. 2023. A Systematic Overexpression Approach Reveals Native Targets to Increase Squalene Production in Synechocystis Sp. PCC 6803. Frontiers in Plant Science 14. doi: 10.3389/fpls.2023.1024981.
Barone GD, Cernava T, Ullmann J, Liu J, Lio E, Germann AT, Nakielski A, Russo DA, Chavkin T, Knufmann K, Tripodi F, Coccetti P, Secundo F, Fu P, Pfleger B, Axmann IM, Lindblad P. Recent developments in the production and utilization of photosynthetic microorganisms for food applications. Heliyon. 2023 Mar 22;9(4):e14708. doi: 10.1016/j.heliyon.2023.e14708.
Mager M, Pineda Hernandez H, Brandenburg F, López-Maury L, McCormick AJ, Nürnberg DJ, Orthwein T, Russo DA, Victoria AJ, Wang X, Zedler JAZ, Branco dos Santos F, Schmelling NM. Interlaboratory Reproducibility in Growth and Reporter Expression in the Cyanobacterium Synechocystis sp. PCC 6803. ACS Synthetic Biology 2023 12 (6), 1823-1835 doi: 10.1021/acssynbio.3c00150.
Germann, AT, Nakielski A, Dietsch M, Petzel T, Moser D, Triesch S, Westhoff P, Axmann IM. 2023. A Systematic Overexpression Approach Reveals Native Targets to Increase Squalene Production in Synechocystis Sp. PCC 6803. Frontiers in Plant Science 14. doi: 10.3389/fpls.2023.1024981.
Barone GD, Cernava T, Ullmann J, Liu J, Lio E, Germann AT, Nakielski A, Russo DA, Chavkin T, Knufmann K, Tripodi F, Coccetti P, Secundo F, Fu P, Pfleger B, Axmann IM, Lindblad P. Recent developments in the production and utilization of photosynthetic microorganisms for food applications. Heliyon. 2023 Mar 22;9(4):e14708. doi: 10.1016/j.heliyon.2023.e14708.
Matuszyńska A, Ebenhöh O, Zurbriggen MD, Ducat DC, Axmann IM. Designing synthetic communities with organism-free modular computational models. ChemRxiv. Cambridge: Cambridge Open Engage; 2022 . doi: 10.26434/chemrxiv-2022-r78kg
Behle A, Dietsch M, Goldschmidt L, Murugathas W, Berwanger LC, Burmester J, Yao L, Brandt D, Busche T, Kalinowski J, Hudson EP, Ebenhöh O, Axmann IM, Machné R. Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis. Nucleic Acids Res. 2022 Dec 9;50(22):12790-12808. doi: 10.1093/nar/gkac1132
Opel F, Axmann IM, Klähn S. The Molecular Toolset and Techniques Required to Build Cyanobacterial Cell Factories. Adv Biochem Eng Biotechnol. 2022 Aug 28. doi: 10.1007/10_2022_210
Klaus O, Hilgers F, Nakielski A, Hasenklever D, Jaeger KE, Axmann IM, Drepper T. Engineering phototrophic bacteria for the production of terpenoids. Curr Opin Biotechnol. 2022 Oct;77:102764. doi: 10.1016/j.copbio.2022.102764
Anna Behle, Ilka M. Axmann. pSHDY: A New Tool for Genetic Engineering of Cyanobacteria DOI: 10.1007/978-1-0716-1791-5_4
Dietsch M, Behle A, Westhoff P, Axmann IM (2021) Metabolic engineering of Synechocystis sp. PCC 6803 for the photoproduction of the sesquiterpene valence. In: Metabolic Engineering Communications, Volume 13, December 2021; doi: 10.1016/j.mec.2021.e00178
Schmelling NM, Scheurer N, Köbler C, Wilde A, Axmann IM (2021) Diversity of Timing Systems in Cyanobacteria and Beyond. In: Johnson CH, Rust MJ (eds) Circadian Rhythms in Bacteria and Microbiomes. Springer, Cham; doi: 10.1007/978-3-030-72158-9_10
Behle A, Saake P, Germann AT, Dienst D, Axmann IM. Comparative dose-response analysis of inducible promoters in cyanobacteria. ACS Synth. Biol. 2020 March 5; doi: 10.1021/acssynbio.9b00505
Wiegard A, Köbler C, Oyama K, Dorrich AK, Azai C, Terauchi K, Wilde A, Axmann IM. Synechocystis KaiC3 displays temperature and KaiB dependent ATPase activity and is important for growth in darkness. J Bacteriol. 2020 January 29; Vol. 202: e00478-19, doi: 10.1128/JB.00478-19
Pauly M, Gawenda N, Wagner C, Fischbach P, Ramírez V, Axmann IM, Voiniciuc C. The Suitability of Orthogonal Hosts to Study Plant Cell Wall Biosynthesis. Plants. 2019 November 17; Vol. 8, 11: 516, doi: 10.3390/plants8110516
Snijder J and Axmann IM. The Kai-Protein Clock — Keeping Track of Cyanobacteria’s Daily Life. In: Harris J, Marles-Wright J (eds) Macromolecular Protein Complexes II: Structure and Function. Subcellular Biochemistry, Springer, Cham. 2019; Vol 93., pp 359-391, doi: 10.1007/978-3-030-28151-9_12
Unger C, Lokmer N, Lehmann D, Axmann IM. Detection of phenol contamination in RNA samples and its impact on qRT-PCR results. Analytical Biochemistry. 2019 April 15; Vol. 8, pp 49-52, doi: 10.1016/j.ab.2019.02.002
Schmelling NM and Axmann IM. Computational modelling unravels the precise clockwork of cyanobacteria. Interface Focus 2018 September 4; Vol. 571: 20180038, doi: 10.1098/rsfs.2018.0038
Senoussi A, Lee Tin Wah J, Shimizu Y, Robert J, Jaramillo A, Findeiss S, Axmann IM, Estevez-Torres A. Quantitative Characterization of Translational Riboregulators Using an In Vitro Transcription–Translation System. ACS Synth. Biol. 2018 April 4; Vol. 7:5, pp 1269–1278, doi: 10.1021/acssynbio.7b00387
Loeschcke A, Dienst D, Wewer V, Hage-Hülsmann J, Dietsch M, Kranz-Finger S, Hüren V, Metzger S, Urlacher VB, Gigolashvili T, Kopriva S, Axmann IM, Drepper T, Jaeger KE. The photosynthetic bacteria Rhodobacter capsulatus and Synechocystis sp. PCC 6803 as new hosts for cyclic plant triterpene biosynthesis. PLoS One. 2017 Dec 27; Vol. 12:12, doi: 10.1371/journal.pone.0189816
Heilmann B, Hakkila K, Georg J, Tyystjaervi T, Hess WR, Axmann IM, Dienst D. 6S RNA plays a role in recovery from nitrogen depletion in Synechocystis sp. PCC 6803. BMC Microbiology. 2017 Dec 8; Vol. 17:229. doi: 10.1186/s12866-017-1137-9
Schmelling NM, Lehmann R, Chaudhury P, Beck C, Albers SV, Axmann IM, Wiegard A. Minimal tool set for a prokaryotic circadian clock. BMC Evolutionary Biology. 2017 Jul 21; Vol. 17, 1:169. doi: 10.1186/s12862-017-0999-7
Snijder J, Schuller JM, Wiegard A, Lössl P, Schmelling N, Axmann IM, Plitzko JM, Förster F, Heck AJ. Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state. Science. 2017 Mar 17; Vol. 355, 6330:1181-1184. doi: 10.1126/science.aag3218
Guerreiro AC, Penning R, Raaijmakers LM, Axmann IM, Heck AJ, Altelaar AF. Monitoring light/dark association dynamics of multi-protein complexes in cyanobacteria using size exclusion chromatography-based proteomics. J Proteomics. 2016 Jun 16;142:33-44. doi: 10.1016/j.jprot.2016.04.030
Amos M, Axmann IM, Blüthgen N, de la Cruz F, Jaramillo A, Rodriguez-Paton A, Simmel F. Bacterial computing with engineered populations. Philos Trans A Math Phys Eng Sci. 2015 Jul 28;373(2046). doi: 10.1098/rsta.2014.0218
Beck C, Hertel S, Rediger A, Lehmann R, Wiegard A, Kölsch A, Heilmann B, Georg J, Hess WR, Axmann IM. Daily expression pattern of protein-encoding genes and small noncoding RNAs in Synechocystis sp. strain PCC 6803. Appl Environ Microbiol. 2014 Sep;80(17):5195-206. doi: 10.1128/AEM.01086-14
Guerreiro AC, Benevento M, Lehmann R, van Breukelen B, Post H, Giansanti P, Maarten Altelaar AF, Axmann IM, Heck AJ. Daily rhythms in the cyanobacterium Synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins. Mol Cell Proteomics. 2014 Aug;13(8):2042-55. doi: 10.1074/mcp.M113.035840
Snijder J, Burnley RJ, Wiegard A, Melquiond AS, Bonvin AM, Axmann IM, Heck AJ. Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction. Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1379-84. doi: 10.1073/pnas.1314326111
Axmann IM, Hertel S, Wiegard A, Dörrich AK, Wilde A. Diversity of KaiC-based timing systems in marine Cyanobacteria. Mar Genomics. 2014 Apr;14:3-16. doi: 10.1016/j.margen.2013.12.006
Lehmann R, Machné R, Georg J, Benary M, Axmann IM, Steuer R. How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis. BMC Bioinformatics. 2013 Apr 21;14:133. doi: 10.1186/1471-2105-14-133
Hertel S, Brettschneider C, Axmann IM. Revealing a two-loop transcriptional feedback mechanism in the cyanobacterial circadian clock. PLoS Comput Biol. 2013;9(3):e1002966. doi: 10.1371/journal.pcbi.1002966
Wiegard A, Dörrich AK, Deinzer H, Beck C, Wilde A, Holtzendorff J, Axmann IM. Biochemical analysis of three putative KaiC clock proteins from Synechocystis sp. PCC 6803 suggests their functional divergence. Microbiology. 2013 May;159(Pt 5):948-58. doi: 10.1099/mic.0.065425-0
Schmiedel JM, Axmann IM, Legewie S. Multi-target regulation by small RNAs synchronizes gene expression thresholds and may enhance ultrasensitive behavior. PLoS One. 2012;7(8):e42296. doi: 10.1371/journal.pone.0042296
Rediger A, Geissen R, Steuten B, Heilmann B, Wagner R, Axmann IM. 6S RNA - an old issue became blue-green. Microbiology. 2012 Oct;158(Pt 10):2480-91. doi: 10.1099/mic.0.058958-0
Beck C, Knoop H, Axmann IM, Steuer R. The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. BMC Genomics. 2012 Feb 2;13:56. doi: 10.1186/1471-2164-13-56
Brettschneider C, Rose RJ, Hertel S, Axmann IM, Heck AJ, Kollmann M. A sequestration feedback determines dynamics and temperature entrainment of the KaiABC circadian clock. Mol Syst Biol. 2010 Jul 13;6:389. doi: 10.1038/msb.2010.44
Wilde A, Axmann IM. Wie messen Bakterien die Zeit? BioSpektrum. Mai 2010.
Axmann IM, Dühring U, Seeliger L, Arnold A, Vanselow JT, Kramer A, Wilde A. Biochemical evidence for a timing mechanism in Prochlorococcus. J Bacteriol. 2009 Sep;191(17):5342-7. doi: 10.1128/JB.00419-09
Legewie S, Dienst D, Wilde A, Herzel H, Axmann IM. Small RNAs establish delays and temporal thresholds in gene expression. Biophys J. 2008 Oct;95(7):3232-8. doi: 10.1529/biophysj.108.133819
Axmann IM, Legewie S, Herzel H. A minimal circadian clock model. Genome Inform. 2007;18:54-64. doi: 10.11234/gi1990.18.54
Kiełbasa SM, Herzel H, Axmann IM. Regulatory elements of marine cyanobacteria. Genome Inform. 2007;18:1-11. doi: 10.11234/gi1990.18.1
Voss B, Gierga G, Axmann IM, Hess WR. A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria. BMC Genomics. 2007 Oct 17;8:375. doi: 10.1186/1471-2164-8-375
Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R, Hess WR, Church GM, Chisholm SW. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature. 2007 Sep 6;449(7158):83-6. doi: 10.1038/nature06130
Axmann IM, Holtzendorff J, Voss B, Kensche P, Hess WR. Two distinct types of 6S RNA in Prochlorococcus. Gene. 2007 Dec 30;406(1-2):69-78. doi: 10.1016/j.gene.2007.06.011
Clodong S, Dühring U, Kronk L, Wilde A, Axmann I, Herzel H, Kollmann M. Functioning and robustness of a bacterial circadian clock. Mol Syst Biol. 2007;3:90. doi: 10.1038/msb4100128
Dühring U, Axmann IM, Hess WR, Wilde A. An internal antisense RNA regulates expression of the photosynthesis gene isiA. Proc Natl Acad Sci U S A. 2006 May 2;103(18):7054-8. doi: 10.1073/pnas.0600927103
Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, Barbe V, Duprat S, Galperin MY, Koonin EV, Le Gall F, Makarova KS, Ostrowski M, Oztas S, Robert C, Rogozin IB, Scanlan DJ, Tandeau de Marsac N, Weissenbach J, Wincker P, Wolf YI, Hess WR. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):10020-5. doi: 10.1073/pnas.1733211100
Vogel J, Axmann IM, Herzel H, Hess WR. Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4. Nucleic Acids Res. 2003 Jun 1;31(11):2890-9. pubmed ID: PMC156731
