Max Planck Institute for Terrestrial Microbiology

Publications

2025

Journal Article

Podolski, A.; Lindeboom, T. A.; Präve, L.; Dehghan, M.; Minas, H. A.; Kranz, J.; Schindler, D.; Bode, H. B.: High-Throughput Engineering and Modification of Non-Ribosomal Peptide Synthetases Based on Golden Gate Assembly. Angewandte Chemie International Edition, e202508967 (2025)

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Journal Article

de Vries, J.; Lindeboom, T. A.; de Vries, S. T.; Schindler, D.; Hoffmann, S. A.: Standardized modular assembly of polycistronic operons with modular cloning (MoClo) using the in-cloning toolkit. Journal of Visualized Experiments (223), e68103 (2025)

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Journal Article

Xu, W.; Jalomo-Khayrova, E.; Gumerov, V. M.; Ross, P. A.; Köbel, T. S.; Schindler, D.; Bange, G.; Zhulin, I. B.; Sourjik, V.: Specificities of chemosensory receptors in the human gut microbiota. Proceedings of the National Academy of Sciences of the United States of America 122 (35), e2508950122 (2025)

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Review Article

Georg, J.; Berghoff, B. A.; Schindler, D.: Harnessing small RNAs as synthetic post-transcriptional regulators in bacteria. ACS Synthetic Biology 14 (7), pp. 2405 - 2417 (2025)

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Book Chapter

de Vries, S. T.; Kley, L.; Schindler, D.: Use of a Golden Gate plasmid set enabling scarless MoClo-compatible transcription unit assembly. In: Golden Gate Cloning. Methods in Molecular Biology, Vol. 2850, pp. 105 - 131 (Ed. Schindler, D.). Humana, New York, NY (2025)

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Book Chapter

Köbel, T. S.; Schindler, D.: Automation and miniaturization of Golden Gate DNA Assembly reactions using acoustic dispensers. In: Golden Gate Cloning. Methods in Molecular Biology, Vol. 2850, pp. 149 - 169 (Ed. Schindler, D.). Humana, New York, NY (2025)

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Book Chapter

Ramírez Rojas, A. A.; Brinkmann, C. K.; Schindler, D.: Validation of Golden Gate Assemblies using highly multiplexed nanopore amplicon sequencing. In: Golden Gate Cloning. Methods in Molecular Biology, Vol. 2850, pp. 171 - 196 (Ed. Schindler, D.). Humana, New York, NY (2025)

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2024

Journal Article

Sendker, F. L.; Schlotthauer, T. J.; Mais, C.-N.; Lo, Y. K.; Girbig, M.; Bohn, S.; Heimerl, T.; Schindler, D.; Weinstein, A.; Metzger, B. P. H. et al.; Thornton, J. W.; Pillai, A.; Bange, G.; Schuller, J. M.; Hochberg, G. K. A.: Frequent transitions in self-assembly across the evolution of a central metabolic enzyme. Nature Communications 15 (1), 10515 (2024)

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Journal Article

de Vries, S. T.; Köbel, T. S.; Sanal, A.; Schindler, D.: In- & Out-Cloning: plasmid toolboxes for scarless transcription unit and modular Golden Gate acceptor plasmid assembly. Synthetic Biology 9 (1), ysae016 (2024)

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Journal Article

He, H.; Gómez-Coronado, P. A.; Zarzycki, J.; Barthel, S.; Kahnt, J.; Claus, P.; Klein, M.; Klose, M.; de Crécy-Lagard, V.; Schindler, D. et al.; Paczia, N.; Glatter, T.; Erb, T. J.: Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies. Nature Communications 15 (1), 8898 (2024)

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Journal Article

Pozhydaieva, N.; Billau, F. A.; Wolfram-Schauerte, M.; Ramírez Rojas, A. A.; Paczia, N.; Schindler, D.; Höfer, K.: Temporal epigenome modulation enables efficient bacteriophage engineering and functional analysis of phage DNA modifications. PLOS Genetics 20 (9), e1011384 (2024)

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Journal Article

Su, L.; Huber, E. M.; Westphalen, M.; Gellner, J.; Bode, E.; Köbel, T.; Grün, P.; Alanjary, M. M.; Glatter, T.; Cirnski, K. et al.; Müller, R.; Schindler, D.; Groll, M.; Bode, H. B.: Isofunctional but structurally different methyltransferases for dithiolopyrrolone diversification. Angewandte Chemie International Edition, e202410799 (2024)

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Journal Article

Brück, M.; Köbel, T. S.; Dittmar, S.; Ramírez Rojas, A. A.; Georg, J.; Berghoff, B. A.; Schindler, D.: A library-based approach allows systematic and rapid evaluation of seed region length and reveals design rules for synthetic bacterial small RNAs. iScience 27 (9), 110774 (2024)

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Book Chapter

Zumkeller, C.; Schindler, D.; Felder, J.; Waldminghaus, T.: Modular Assembly of Synthetic Secondary Chromosomes. In: Bacterial Chromatin. Methods in Molecular Biology,, Vol. 2819, 2819 Ed., pp. 157 - 187 (Ed. Dame, R. T.). Humana, New York, NY (2024)

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Journal Article

Szymanski, E. A.; Schindler, D.: A (metaphorical) moment for RNA-based biotechnology?: Current metaphors for RNA limit development of and public communication about RNA-based technologies. EMBO Reports 25, pp. 3182 - 3186 (2024)

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Journal Article

Ramming, L.; Stukenberg, D.; Sanchez Olmos, M. d. C.; Glatter, T.; Becker, A.; Schindler, D.: Rationally designed chromosome fusion does not prevent rapid growth of Vibrio natriegens. Communications Biology 7 (1), 519 (2024)

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Journal Article

Lindeboom, T. A.; Sanchez Olmos, M. d. C.; Schulz, K.; Brinkmann, C. K.; Ramírez Rojas, A. A.; Hochrein, L.; Schindler, D.: An optimized genotyping workflow for identifying highly SCRaMbLEd synthetic yeasts. ACS Synthetic Biology 13 (4), pp. 1116 - 1127 (2024)

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Journal Article

Sendker, F. L.; Lo, Y. K.; Heimerl, T.; Bohn, S.; Persson, L. J.; Mais, C.-N.; Sadowska, W.; Paczia, N.; Nußbaum, E.; del Carmen Sánchez Olmos, M. et al.; Forchhammer, K.; Schindler, D.; Erb, T. J.; Benesch, J. L. P.; Marklund, E. G.; Bange, G.; Schuller, J. M.; Hochberg, G. K. A.: Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature 628 (8009), pp. 894 - 900 (2024)

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Preprint

Wolfram-Schauerte, M.; Moskalchuk, A.; Pozhydaieva, N.; Ramírez Rojas, A. A.; Schindler, D.; Kaiser, S.; Paczia, N.; Höfer, K.: T4 phage RNA is NAD-capped and alters the NAD-cap epitranscriptome of Escherichia coli during infection through a phage-encoded decapping enzyme. bioRxiv: the preprint server for biology, 2024.04.04.588121 (2024)

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Book Chapter

Brück, M.; Berghoff, B. A.; Schindler, D.: In Silico Design, In Vitro Construction, and In Vivo Application of Synthetic Small Regulatory RNAs in Bacteria. In: Synthetic Biology. Methods in Molecular Biology, Vol. 2760 (Ed. Braman, J. C.). Humana, New York, NY. (2024)

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Journal Article

Ramírez Rojas, A. A.; Brinkmann, C. K.; Köbel, T. S.; Schindler, D.: DuBA.flow─A low-cost, long-read amplicon sequencing workflow for the validation of synthetic DNA constructs. ACS Synthetic Biology (2024)

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Journal Article

Cheng, L.; Zhao, S.; Li, T.; Hou, S.; Luo, Z.; Xu, J.; Yu, W.; Jiang, S.; Monti, M.; Schindler, D. et al.; Zhang, W.; Hou, C.; Ma, Y.; Cai, Y.; Boeke, J. D.; Dai, J.: Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae. Nature Communications 15 (1), 770 (2024)

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Preprint

Su, L.; Huber, E. M.; Westphalen, M.; Gellner, J.; Bode, E.; Köbel, T.; Grün, P.; Alanjary, M. M.; Glatter, T.; Schindler, D. et al.; Groll, M.; Bode, H. B.: Identification, structure and function of the methyltransferase involved in the biosynthesis of the dithiolopyrrolone antibiotic xenorhabdin. bioRxiv: the preprint server for biology, 2024.01.12.575338 (2024)

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Journal Article

Schindler, D.; Walker, R. S.K.; Cai, Y.: Methodological advances enabled by the construction of a synthetic yeast genome. Cell Reports Methods 4 (4), 100761 (2024)

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2023

Journal Article

Philipp, N.; Brinkmann, C. K.; Georg, J.; Schindler, D.; Berghoff, B. A.: DIGGER-Bac: prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria. Bioinformatics 39 (5), btad285 (2023)

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Journal Article

Abramczyk, D.; Sanchez Olmos, M. d. C.; Ramírez Rojas, A. A.; Schindler, D.; Robertson, D.; McColm, S.; Marston, A. L.; Barlow, P. N.: A supernumerary synthetic chromosome in Komagataella phaffii as a repository for extraneous genetic material. Microbial Cell Factories 22 (1), 259 (2023)

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Journal Article

Luo, S.; Diehl, C.; He, H.; Bae, Y.; Klose, M.; Claus, P.; Cortina, N. S.; Fernandez, C. A.; Schulz-Mirbach, H. A. M.; McLean, R. et al.; Ramírez Rojas, A. A.; Schindler, D.; Paczia, N.; Erb, T. J.: Construction and modular implementation of the THETA cycle for synthetic CO₂ fixation. Nature Catalysis 6 (12), pp. 1228 - 1240 (2023)

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Journal Article

Schindler, D.; Walker, R. S.K.; Jiang, S.; Brooks, A. N.; Wang, Y.; Müller, C. A.; Cockram, C.; Luo, Y.; García, A.; Schraivogel, D. et al.; Mozziconacci, J.; Pena, N.; Assari, M.; Olmos, S.; Carmen, M. d.; Zhao, Y.; Ballerini, A.; Blount, B. A.; Cai, J.; Ogunlana, L.; Liu, W.; Jönsson, K.; Abramczyk, D.; Garcia-Ruiz, E.; Turowski, T. W.; Swidah, R.; Ellis, T.; Pan, T.; Antequera, F.; Shen, Y.; Nieduszynski, C. A.; Koszul, R.; Dai, J.; Steinmetz, L. M.; Boeke, J. D.; Cai, Y.: Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell 186 (24), pp. 5237 - 5253.e22 (2023)

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Journal Article

Shen, Y.; Gao, F.; Wang, Y.; Wang, Y.; Zheng, J.; Gong, J.; Zhang, J.; Luo, Z.; Schindler, D.; Deng, Y. et al.; Ding, W.; Lin, T.; Swidah, R.; Zhao, H.; Jiang, S.; Zeng, C.; Chen, S.; Chen, T.; Wang, Y.; Luo, Y.; Mitchell, L.; Bader, J. S.; Zhang, G.; Shen, X.; Wang, J.; Fu, X.; Dai, J.; Boeke, J. D.; Yang, H.; Xu, X.; Cai, Y.: Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast. Cell genomics 3 (11), 100364 (2023)

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Journal Article

Steube, N.; Moldenhauer, M.; Weiland, P.; Saman, D.; Kilb, A.; Ramírez Rojas, A. A.; Garg, S.; Schindler, D.; Graumann, P. L.; Benesch, J. L. P. et al.; Bange, G.; Friedrich, T.; Hochberg, G. K. A.: Fortuitously compatible protein surfaces primed allosteric control in cyanobacterial photoprotection. Nature Ecology & Evolution 7, pp. 756 - 767 (2023)

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2022

Journal Article

Ramírez Rojas, A. A.; Swidah, R.; Schindler, D.: Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges. Frontiers in Bioengineering and Biotechnology 10, 982975 (2022)

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Journal Article

Koebel, T. S.; Palhares, R. M.; Fromm, C.; Szymanski, W. G.; Angelidou, G.; Glatter, T.; Georg, J.; Berghoff, B. A.; Schindler, D.: An easy-to-use plasmid toolset for efficient generation and benchmarking of synthetic small RNAs in bacteria. ACS Synthetic Biology 11 (9), pp. 2989 - 3003 (2022)

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2021

Journal Article

Ong, J. Y.; Swidah, R.; Monti, M.; Schindler, D.; Dai, J.; Cai, Y.: SCRaMbLE: A study of its robustness and challenges through enhancement of Hygromycin B resistance in a semi-synthetic yeast. Bioengineering 8 (3), 42 (2021)

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Journal Article

Luo, Z.; Yu, K.; Xie, S.; Monti, M.; Schindler, D.; Fang, Y.; Zhao, S.; Liang, Z.; Jiang, S.; Luan, M. et al.; Xiao, C.; Cai, Y.; Dai, J.: Compacting a synthetic yeast chromosome arm. Genome Biology: Biology for the Post-Genomic Era 22 (1), 5 (2021)

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2020

Journal Article

Schindler, D.: Genetic Engineering and Synthetic Genomics in Yeast to Understand Life and Boost Biotechnology. Bioengineering-Basel 7 (4), pp. 137 - Article No.: 137 (2020)

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Journal Article

Zhao, Y.; Yao, Z.; Ploessl, D.; Ghosh, S.; Monti, M.; Schindler, D.; Gao, M.; Cai, Y.; Qiao, M.; Yang, C. et al.; Cao, M.; Shao, Z.: Leveraging the Hermes Transposon to Accelerate the Development of Nonconventional Yeast-based Microbial Cell Factories. ACS SYNTHETIC BIOLOGY 9 (7), pp. 1736 - 1752 (2020)

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2018

Journal Article

Bruhn, M.; Schindler, D.; Kemter, F. S.; Wiley, M. R.; Chase, K.; Koroleva, G. I.; Palacios, G.; Sozhamannan, S.; Waldminghaus, T.: Functionality of Two Origins of Replication in Vibrio cholerae Strains With a Single Chromosome. FRONTIERS IN MICROBIOLOGY 9, 2932 (2018)

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Journal Article

Schindler, D.; Dai, J.; Cai, Y.: Synthetic genomics: a new venture to dissect genome fundamentals and engineer new functions. CURRENT OPINION IN CHEMICAL BIOLOGY 46, pp. 56 - 62 (2018)

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Journal Article

Schallopp, N.; Milbredt, S.; Sperlea, T.; Kemter, F. S.; Bruhn, M.; Schindler, D.; Waldminghaus, T.: Establishing a System for Testing Replication Inhibition of the Vibrio cholerae Secondary Chromosome in Escherichia coli. ANTIBIOTICS-BASEL 7 (1), 3 (2018)

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Conference Paper

Zumkeller, C.; Schindler, D.; Waldminghaus, T.: Modular Assembly of Synthetic Secondary Chromosomes. In: BACTERIAL CHROMATIN: Methods and Protocols, pp. 71 - 94. (2018)

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2016

Journal Article

Messerschmidt, S. J.; Schindler, D.; Zumkeller, C. M.; Kemter, F. S.; Schallopp, N.; Waldminghaus, T.: Optimization and characterization of the synthetic secondary chromosome synVicII in Escherichia coli. FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY 4, 96 (2016)

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Journal Article

Schindler, D.; Milbredt, S.; Sperlea, T.; Waldminghaus, T.: Design and Assembly of DNA Sequence Libraries for Chromosomal Insertion in Bacteria Based on a Set of Modified MoClo Vectors. ACS SYNTHETIC BIOLOGY 5 (12), pp. 1362 - 1368 (2016)

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2015

Journal Article

Schindler, D.; Waldminghaus, T.: Synthetic chromosomes. FEMS MICROBIOLOGY REVIEWS 39 (6), pp. 871 - 891 (2015)

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Journal Article

Messerschmidt, S. J.; Kemter, F. S.; Schindler, D.; Waldminghaus, T.: Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae. SI 10 (2), pp. 302 - 314 (2015)

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2014

Journal Article

Schindler, D.; Nowrousian, M.: The polyketide synthase gene pks4 is essential for sexual development and regulates fruiting body morphology in Sordaria macrospora. FUNGAL GENETICS AND BIOLOGY 68, pp. 48 - 59 (2014)

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2013

Journal Article

Schindler, D.; Waldminghaus, T.: "Non-canonical protein-DNA interactions identified by ChIP are not artifacts": response. BMC GENOMICS 14, 638 (2013)

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Journal Article

Gesing, S.; Schindler, D.; Nowrousian, M.: Suppression subtractive hybridization and comparative expression analysis to identify developmentally regulated genes in filamentous fungi. JOURNAL OF BASIC MICROBIOLOGY 53 (9), pp. 742 - 751 (2013)

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2012

Journal Article

Gesing, S.; Schindler, D.; Fraenzel, B.; Wolters, D.; Nowrousian, M.: The histone chaperone ASF1 is essential for sexual development in the filamentous fungus Sordaria macrospora. MOLECULAR MICROBIOLOGY 84 (4), pp. 748 - 765 (2012)

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