Welcome to the DFG SPP2141

CRISPR-Cas functions beyond defence


One of the most exciting breakthroughs in biology in the past decade has been the discovery of the CRISPR-Cas system. Initially identified as a prokaryotic defence system, we now know that defence is just one of many functions of this molecular machine. Thus, the prevailing view of CRISPR-Cas as a defence system is too narrow. Other important cellular processes are carried out by the CRISPR-Cas system, such as virulence regulation, DNA repair and the regulation of group behaviour, to name only a few. In some cases, CRISPR- Cas systems may even have completely lost their immune-related functions. At this time, we have barely begun to understand the full biological potential of this system. The newly revealed functions of the CRISPR-Cas system promise exciting biological discoveries and surprising insights into the new activities and will open several novel avenues of research. Thus far, the new CRISPR-Cas functions have primarily been discovered fortuitously and systematic approaches to detect new functions are lacking. The SPP2141 aims at finding new CRISPR-Cas fuctions beyond defence using a systematic coordinated approach with 21 interdisciplinary groups. 

CRISPR-Cas functions beyond the defence:
Functions of the CRISPR-Cas system in virulence and group behaviour have been described and are shown here. To date, the molecular details underlying these functions are not known. Figure modified from (Ratner, H.K. et al. (2015) I can see CRISP now, even when phage are gone: a view on alternative CRISPR-Cas functions from the prokaryotic envelope. Curr Opin Infect Dis. 28, 267-74.)

Prof. Dr. Anita Marchfelder


Coordinating commitee:
Prof. Dr. Rolf Backofen, Albert-Ludwigs-Universität, Freiburg
Prof. Dr. Wolfgang R. Hess, Albert-Ludwigs-Universität

Dr. Lennart Randau, Max-Plank-Institut für terrestrische Mikrobiologie, Marburg

Prof. Dr. Ruth Schmitz-Streit, Christian-Albrechts-Universität, Kiel



  • Projects

    Prof. Dr. Gert Bange, Philipps-University Marburg
    Structure, mechanism and function of class I CRISPR-Cas systems
    Dr. Franz Baumdicker, Albert-Ludwigs-Universität, Freiburg
    Evolutionary dynamics and phylogenetic inference of CRISPR systems in prokaryotic populations
    Prof. Dr. Chase Beisel, HIRI, Würzburg
    Functional characterization of extensively self-targeting CRISPR-Cas systems in the bacterial plant pathogen Xanthomonas albilineans
    Dr. Ulrike Endesfelder, Max Planck Institute for Terrestrial Microbiology, Marburg
    Studying protein organization and dynamics of the Type I-Fv CRISPR-Cas system of Shewanella putrefaciens CN-32 at a high spatiotemporal resolution in living cells
    Prof. Dr. Uri Gophna, Tel Aviv University, Isreal
    The effects of CRISPR-Cas systems on microbial genetic diversity
    Prof. Dr. Dina Grohmann, Institut für Biochemie, Genetik und Mikrobiologie,Regensburg
    Single-molecule analysis of non-canonical Cas1 and Cas9 complexes involved DNA repair and posttranscriptional gene regulation
    Prof. Dr. Wolfgang Hess, Albert-Ludwigs-Universität, Freiburg
    Cross-talk and extensive rewiring of CRISPR-Cas systems with the cellular regulatory machinery in Synechocystis sp. PCC 6803
    Prof. Dr. Gabriele Klug, Justus-Liebig-Universität, Gießen
    CRISPR-Cas functions in the stress response of Rhodobacter capsulatus
    Prof. Dr. Anita Marchfelder, Universität Ulm
    CRISPR-Cas functions beyond defence in haloarchaea
    Prof. Dr. Alice McHardy, Braunschweig
    Learning structures in the CRISPR-Cas system using deep learning architectures
    Dr. Lennart Randau, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg
    Functional analysis of Shewanella putrefaciens Type I-Fv and Aromatoleum aromaticum Type IV CRISPR-Cas ribonucleoprotein complexes
    Prof. Dr. Ruth Schmitz-Streit/ Dr. Anne Kupczok, Christian-Albrechts-Universität Kiel
    The Casposon of Methanosarcina mazei Gö1 - function and evolution
    Dr. Sabine Schneider, Technical University of Munich, Garching
    Elucidation of the molecular mechanism of Cas endonucleases from bacteria and cyanobacteria
    Priv.-Doz. Dr. Dr. Christoph Schoen, Julius-Maximilians-Universität Würzburg
    The CRISPR-Cas system in Neisseria meningitidis and its potential role in host cell adhesion
    Prof. Ralf Seidel, Universität Leipzig,
    RNA processing and activation of Type III-A CRISPR-Cas systems
    Prof. Dr. Cynthia Sharma, Julius-Maximilians-Universität Würzburg
    Mechanisms and functions of endogenous RNA-targeting by CRISPR-Cas9 in Campylobacter jejuni
    Prof. Dr. Björn Voß, Universität Stuttgart
    Metagenomic data mining for the Analysis of CRISPR-Cas systems
    Prof. Dr. Annegret Wilde, Albert-Ludwigs-Universität, Freiburg
    Natural functions of CRISPR-Cas systems in Cyanobacteria
    Z projects
    Prof. Dr. Rolf Backofen, Albert-Ludwigs-Universität, Freiburg
    CRISPR Bioinformatics
    Prof. Dr. Henning Urlaub, Max-Planck-Institut für biophysikalische Chemie,
    Mass spectrometric proteomic and structural proteomics on CRISPR-Cas of archaea and bacteria
    Public Outreach Module
    Dr. Heike Ziegler & Prof. Dr. Wolfgang Nellen, Universität Kassel
    CRISPR-Cas - more than defense
    Associated groups
    Prof. Dr. Emmanuelle Charpentier, Max-Planck-Institut für Infektionsbiologie, Berlin
    Prof. Dr. Qunxin She, University of Copenhagen
    Prof. Dr. Barbara Spellerberg, Universitätsklinikum Ulm


  • Publications


     Selective Enrichment of Slow-Growing Bacteria in a Metabolism-Wide CRISPRi Library with a TIMER Protein. Beuter D, Gomes-Filho JV, Randau L, Díaz-Pascual F, Drescher K, Link H. ACS Synth Biol. 2018 Nov 16. doi: 10.1021/acssynbio.8b00379.

     Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum. Özcan A, Pausch P, Linden A, Wulf A, Schühle K, Heider J, Urlaub H, Heimerl T, Bange G, Randau L. Nat Microbiol. 2018 Nov 5. doi: 10.1038/s41564-018-0274-8.

     PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures. Gleditzsch D, Pausch P, Müller-Esparza H, Özcan A, Guo X, Bange G, Randau L. RNA Biol. 2018 Sep 18:1-14. doi: 10.1080/15476286.2018.1504546.

     CRISPR-Cas systems in multicellular cyanobacteria. Hou S, Brenes-Álvarez M, Reimann V, Alkhnbashi OS, Backofen R, Muro-Pastor AM, Hess WR. RNA Biol. 2018 Aug 15:1-12. doi: 10.1080/15476286.2018.1493330.

     CRISPR-Based Technologies for Metabolic Engineering in Cyanobacteria. Behler J, Vijay D, Hess WR, Akhtar MK. Trends Biotechnol. 2018 Oct;36(10):996-1010. doi: 10.1016/j.tibtech.2018.05.011. Epub 2018 Jun 21. Review.

     Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families. Shah SA, Alkhnbashi OS, Behler J, Han W, She Q, Hess WR, Garrett RA, Backofen R. RNA Biol. 2018 Jun 19:1-13. doi: 10.1080/15476286.2018.1483685.

     Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation. Kieper SN, Almendros C, Behler J, McKenzie RE, Nobrega FL, Haagsma AC, Vink JNA, Hess WR, Brouns SJJ. Cell Rep. 2018 Mar 27;22(13):3377-3384. doi: 10.1016/j.celrep.2018.02.103.

     Biochemical analysis of the Cas6-1 RNA endonuclease associated with the subtype I-D CRISPR-Cas system in Synechocystis sp. PCC 6803. Jesser R, Behler J, Benda C, Reimann V, Hess WR. RNA Biol. 2018 Mar 26:1-11. doi: 10.1080/15476286.2018.1447742.

    The host-encoded RNase E endonuclease as the crRNA maturation enzyme in a CRISPR-Cas subtype III-Bv system.Behler J, Sharma K, Reimann V, Wilde A, Urlaub H, Hess WR.Nat Microbiol. 2018 Mar;3(3):367-377. doi: 10.1038/s41564-017-0103-5. Epub 2018 Feb 5.

     The independent loss model with ordered insertions for the evolution of CRISPR spacers. Baumdicker F, Huebner AMI, Pfaffelhuber P. Theor Popul Biol. 2018 Feb;119:72-82. doi: 10.1016/j.tpb.2017.11.001. Epub 2017 Nov 22.

     CRISPR tool puts RNA on the record. Beisel CL. Nature. 2018 Oct;562(7727):347-349. doi: 10.1038/d41586-018-06869-1.

     The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays. Liao C, Slotkowski RA, Achmedov T, Beisel CL. RNA Biol. 2018 Oct 12:1-9. doi: 10.1080/15476286.2018.1526537.

     Advances in CRISPR Technologies for Microbial Strain Engineering. Alper HS, Beisel CL. Biotechnol J. 2018 Sep;13(9):e1800460. doi: 10.1002/biot.201800460.

     Genome Editing with CRISPR-Cas9 in Lactobacillus plantarum Revealed That Editing Outcomes Can Vary Across Strains and Between Methods. Leenay RT, Vento JM, Shah M, Martino ME, Leulier F, Beisel CL. Biotechnol J. 2018 Aug 29:e1700583. doi: 10.1002/biot.201700583.

     CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9. Dugar G, Leenay RT, Eisenbart SK, Bischler T, Aul BU, Beisel CL, Sharma CM. Mol Cell. 2018 Mar 1;69(5):893-905.e7. doi: 10.1016/j.molcel.2018.01.032.

     A detailed cell-free transcription-translation-based assay to decipher CRISPR protospacer-adjacent motifs. Maxwell CS, Jacobsen T, Marshall R, Noireaux V, Beisel CL. Methods. 2018 Jul 1;143:48-57. doi: 10.1016/j.ymeth.2018.02.016. Epub 2018 Feb 24.

    Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System. Marshall R, Maxwell CS, Collins SP, Jacobsen T, Luo ML, Begemann MB, Gray BN, January E, Singer A, He Y, Beisel CL, Noireaux V. Mol Cell. 2018 Jan 4;69(1):146-157.e3. doi: 10.1016/j.molcel.2017.12.007.

    Repeat modularity as a beneficial property of multiple CRISPR-Cas systems. Yair Y, Gophna U. RNA Biol. 2018 Aug 10:1-3. doi: 10.1080/15476286.2018.1474073.

     The nuts and bolts of the Haloferax CRISPR-Cas system I-B. Maier LK, Stachler AE, Brendel J, Stoll B, Fischer S, Haas KA, Schwarz TS, Alkhnbashi OS, Sharma K, Urlaub H, Backofen R, Gophna U, Marchfelder A. RNA Biol. 2018 May 21:1-12. doi: 10.1080/15476286.2018.1460994.

    Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. Clouet-d'Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK. FEMS Microbiol Rev. 2018 Sep 1;42(5):579-613. doi: 10.1093/femsre/fuy016.

    Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei Gö1. Nickel L, Ulbricht A, Alkhnbashi OS, Förstner KU, Cassidy L, Weidenbach K, Backofen R, Schmitz RA. RNA Biol. 2018 Sep 13:1-12. doi: 10.1080/15476286.2018.1514234.

    The CRISPR/Cas system in Neisseria meningitidis affects bacterial adhesion to human nasopharyngeal epithelial cells. Heidrich N, Hagmann A, Bauriedl S, Vogel J, Schoen C. RNA Biol. 2018 Jul 30:1-7. doi: 10.1080/15476286.2018.1486660

    Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in Vitro. Krivoy A, Rutkauskas M, Kuznedelov K, Musharova O, Rouillon C, Severinov K, Seidel R. Nucleic Acids Res. 2018 May 4;46(8):4087-4098. doi: 10.1093/nar/gky219.

    Stable maintenance of the rudivirus SIRV3 in a carrier state in Sulfolobus islandicus despite activation of the CRISPR-Cas immune response by a second virus SMV1. Papathanasiou P, Erdmann S, Leon-Sobrino C, Sharma K, Urlaub H, Garrett RA, Peng X. RNA Biol. 2018 Sep 13:1-9. doi: 10.1080/15476286.2018.1511674.