Publications

Last update: November 2016

List of publications

  • 2016

    Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system. Gleditzsch D, Müller-Esparza H, Pausch P, Sharma K, Dwarakanath S, Urlaub H, Bange G, Randau L. Nucleic Acids Res. 2016  44: 5872-82.

    A Non-Stem-Loop CRISPR RNA Is Processed by Dual Binding Cas6. Shao Y, Richter H, Sun S, Sharma K, Urlaub H, Randau L, Li H. Structure. 2016 24:547-54.

    Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs. Reimann V, Alkhnbashi OS, Saunders SJ, Scholz I, Hein S, Backofen R, Hess WR. Nucleic Acids Res. 2016 Sep 5. pii: gkw786. [Epub ahead of print]

    Characterizing leader sequences of CRISPR loci. Alkhnbashi OS, Shah SA, Garrett RA, Saunders SJ, Costa F, Backofen R. Bioinformatics. 2016 32:i 576-i585.

    Gene Repression in Haloarchaea Using the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas I-B System. Stachler AE, Marchfelder A. J Biol Chem. 2016 291: 15226-42.

    Engineering of temperature- and light-switchable Cas9 variants. Richter F, Fonfara I, Bouazza B, Schumacher CH, Bratovič M, Charpentier E, Möglich A. Nucleic Acids Res. 2016 Oct 15. pii: gkw930. [Epub ahead of print]

    CRISPR-Cas: biology, mechanisms and relevance. Hille F, Charpentier E. Philos Trans R Soc Lond B Biol Sci. 2016 371(1707).

    The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E. Nature. 2016 532: 517-21.

    Adaptation in CRISPR-Cas Systems. Sternberg SH, Richter H, Charpentier E, Qimron U. Mol Cell. 2016 61: 797-808.

    Major and minor crRNA annealing sites facilitate low stringency DNA protospacer binding prior to Type I-A CRISPR-Cas interference in Sulfolobus. Mousaei M, Deng L, She Q, Garrett RA. RNA Biol. 2016 13: 1166-1173.

    Diverse CRISPR-Cas responses and dramatic cellular DNA changes and cell death in pKEF9-conjugated Sulfolobus species. Liu G, She Q, Garrett RA. Nucleic Acids Res. 2016 44: 4233-42.

    Transcriptome changes in STSV2-infected Sulfolobus islandicus REY15A undergoing continuous CRISPR spacer acquisition. León-Sobrino C, Kot WP, Garrett RA. Mol Microbiol. 2016 99:719-28.

    Harnessing Type I and Type III CRISPR-Cas systems for genome editing. Li Y, Pan S, Zhang Y, Ren M, Feng M, Peng N, Chen L, Liang YX, She Q. Nucleic Acids Res. 2016 44: e34.

  • 2015

    Toward Whole-Transcriptome Editing with CRISPR-Cas9. Heckl D, Charpentier E. Mol Cell. 2015 58: 560-2.

    Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. Charpentier E, Richter H, van der Oost J, White MF. FEMS Microbiol Rev. 2015 39: 428-41.

    CRISPR germline engineering--the community speaks. Bosley KS, Botchan M, Bredenoord AL, Carroll D, Charo RA, Charpentier E, Cohen R, Corn J, Doudna J, Feng G, Greely HT, Isasi R, Ji W, Kim JS, Knoppers B, Lanphier E, Li J, Lovell-Badge R, Martin GS, Moreno J, Naldini L, Pera M, Perry AC, Venter JC, Zhang F, Zhou Q. Nat Biotechnol. 2015 33: 478-86.

    DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes. Plagens A, Richter H, Charpentier E, Randau L. FEMS Microbiol Rev. 2015 39: 442-63.

    CRISPR-Cas9: how research on a bacterial RNA-guided mechanism opened new perspectives in biotechnology and biomedicine. Charpentier E. EMBO Mol Med. 2015 7: 363-5.

    An updated evolutionary classification of CRISPR-Cas systems. Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV. Nat Rev Microbiol. 2015 13: 722-36.

    Interference activity of a minimal Type I CRISPR-Cas system from Shewanella putrefaciens. Dwarakanath S, Brenzinger S, Gleditzsch D, Plagens A, Klingl A, Thormann K, Randau L. Nucleic Acids Res. 2015 43: 8913-23.

    Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RH, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H. Methods. 2015 89: 138-48.

    In Vitro Co-reconstitution of Cas Protein Complexes. Plagens A, Randau L. Methods Mol Biol. 2015 1311: 23-33.

    DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes. Plagens A, Richter H, Charpentier E, Randau L. FEMS Microbiol Rev. 2015 39: 442-63.

    The role of Cas8 in type I CRISPR interference. Cass SD, Haas KA, Stoll B, Alkhnbashi OS, Sharma K, Urlaub H, Backofen R, Marchfelder A, Bolt EL. Biosci Rep. 2015 35(3).

    Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RH, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H. Methods. 2015 89: 138-48.

    The Adaptive Immune System of Haloferax volcanii. Maier LK, Dyall-Smith M, Marchfelder A. Life (Basel). 2015 5: 521-37.

    An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein. Maier LK, Stachler AE, Saunders SJ, Backofen R, Marchfelder A. J Biol Chem. 2015 290: 4192-201.

    Investigating CRISPR RNA Biogenesis and Function Using RNA-seq. Heidrich N1, Dugar G, Vogel J, Sharma CM. Methods Mol Biol. 2015 1311: 1-21.

    Archaeal Viruses of the Sulfolobales: Isolation, Infection, and CRISPR Spacer Acquisition. Erdmann S, Garrett RA. Methods Mol Biol. 2015 1311: 223-32.

    CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity. Garrett RA, Shah SA, Erdmann S, Liu G, Mousaei M, León-Sobrino C, Peng W, Gudbergsdottir S, Deng L, Vestergaard G, Peng X, She Q. Life (Basel). 2015 5: 783-817.

    Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR-Cas system.Fusco S, Liguori R, Limauro D, Bartolucci S, She Q, Contursi P. Biochimie. 2015 118: 322-32.

    Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition. Liu T, Li Y, Wang X, Ye Q, Li H, Liang Y, She Q, Peng N. Nucleic Acids Res. 2015 43: 1044-55.

    An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference. Peng W, Feng M, Feng X, Liang YX, She Q. Nucleic Acids Res. 2015 43: 406-17.

  • 2014

    Alkhnbashi OS, Costa F, Shah SA, Garrett RA, Saunders SJ, Backofen R. (2014) CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Bioinformatics. 2014 30:i489-96. doi: 10.1093/bioinformatics/btu459.

    Arslan Z*, Hermanns V*, Wurm R, Wagner R, Pul, Ü (2014) Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system, Nucl Acids Res, 42: 7884-93.

    *These authors contributed equally to this work.

    Benda C, Ebert J, Scheltema RA, Schiller HB, Baumgärtner M, Bonneau F, Mann M, Conti E. (2014) Structural model of a CRISPR RNA-silencing complex reveals the RNA-target cleavage activity in Cmr4. Mol Cell. 56:43-54. doi: 10.1016/j.molcel.2014.09.002.

    Brendel, J., Stoll, B., Lange, S.J., Stachler, A.-E., Maier, L.-K., Sharma, K., Richter ,H., Nickel, L., Schmitz, R.A., Randau, L., Urlaub, H., Allers, T., Backofen, R. and Marchfelder, A. (2014) Cas6 is necessary but not sufficient for a stable crRNA population in Haloferax volcanii, J Biol Chem, 289: 7164-7177.

    Daume M, Plagens A, Randau L. (2014) DNA binding properties of the small cascade subunit Csa5. PLoS One. 2014 9:e105716. doi: 10.1371/journal.pone.0105716. eCollection 2014.

    Erdmann S, Le Moine Bauer S, Garrett RA. (2014) Inter-viral conflicts that exploit host CRISPR immune systems of Sulfolobus. Mol Microbiol: 91:900-17.

    Heidrich N, Dugar G, Vogel J & Sharma CM (2014) Investigating CRISPR RNA biogenesis and function using RNA-seq. In: CRISPR Methods & Protocols, Charpentier E, Lundgren M, (Eds.), Springer Science + Business Media, LLC, in press.

    Hrle A, Maier LK, Sharma K, Ebert J, Basquin C, Urlaub H, Marchfelder A, Conti E. (2014) Structural analyses of the CRISPR protein Csc2 reveal the RNA-binding interface of the type I-D Cas7 family. RNA Biol. 11:1072-82. doi: 10.4161/rna.29893.

    Plagens, A., Tripp, V., Daume, M., Sharma, K., Klingl, A., Hrle, A., Conti, E., Urlaub, H. and Randau, L. (2014) In vitro assembly and activity of an archaeal CRISPR-Cas type I-A Cascade interference complex. Nucl Acids Res, 42: 5125-38.

    Plagens, A. and Randau, L. (2014) Small RNA-guided adaptive immunity: Comment on “Diversity, Evolution, and Therapeutic Applications of small RNAs in Prokaryotic and Eukaryotic Immune Systems” by Cooper and Overstreet. Phys. Life Rev. 11: 139-140.

    Plagens, A and Randau, L. (2014) In vitro co-reconstitution of Cas protein complexes. Meth Mol Biol, in press.

    Pul Ü (2014) Chemical and enzymatic footprint analyses of R-Loop formation by Cascade-crRNA complex. Meth Mol Biol, in press.

    Staals RH, Zhu Y, Taylor DW, Kornfeld JE, Sharma K, Barendregt A, Koehorst JJ, Vlot M, Neupane N, Varossieau K, Sakamoto K, Suzuki T, Dohmae N, Yokoyama S, Schaap PJ, Urlaub H, Heck AJ, Nogales E, Doudna JA, Shinkai A, van der Oost J. (2014) RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus. Mol Cell. 56:518-30. doi: 10.1016/j.molcel.2014.10.005. Epub 2014 Nov 6.

    Vestergaard, G., Garrett, R. A., and Shah, S. A. (2014) CRISPR adaptive immune systems of Archaea. RNA Biol. 11, 156-167.

  • 2013

    Arslan Z, Stratmann T, Wurm R, Wagner R, Schnetz K, Pul Ü (2013) RcsB-BglJ-mediated activation of Cascade operon does not induce the maturation of CRISPR RNAs in E. coli K12. RNA Biol 10: 708-715.

    Arslan Z, Wurm R, Brener O, Ellinger P, Nagel-Steger L, Oesterhelt F, Schmitt L, Willbold D, Wagner R, Gohlke H, Smits S, Pul Ü (2013) Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2. Nucl Acids Res 41: 6347-6359.

    Arslan Z, Westra ER, Wagner R, Pul Ü (2013) Regulation of CRISPR-based immune responses. In: CRISPR-Cas systems: RNA-mediated Adaptive Immunity in Bacteria and Archaea, Barrangou, Rodolphe; van der Oost, John (Eds.), Springer-Verlag X, 93-113.

    Deng L, Garrett RA, Shah SA, Peng X, She Q (2013) A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol Microbiol 87: 1088-1099.

    Dugar, G., Herbig, A., Förstner, K. U., Heidrich, N., Reinhardt, R., Nieselt, K., Sharma, C. M. (2013) High‐Resolution Transcriptome Maps Reveal Strain‐Specific Regulatory Features of Multiple Campylobacter jejuni Isolates. PLoS Genetics, 9(5), e1003495.

    Erdmann, S., S.A. Shah, and R.A. Garrett (2013) SMV1 virus-induced CRISPR spacer acquisition from the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2. Biochem Soc Trans 41, 1449-1458.

    Erdmann, S., B. Chen, X. Huang, L. Deng, C. Liu, S.A. Shah, S.L.M. Bauer, C.L. Sobrino, H. Wang, Y. Wei, Q. She, R.A. Garrett, L. Huang, L. Lin (2013) A novel single-tailed fusiform Sulfolobus virus STSV2 infecting model Sulfolobus species. Extremophiles, in press.

    Fusco,S., Q. She, S. Bartolucci, P. Contursi (2013) Tlys, a novel identified SSV1 transcript expressed in the lysogenic state, encodes for a DNA-binding protein interacting at the promotersof the early genes. J Virol. 87, 5926-5936.

    Heidrich, N., Vogel J (2013) CRISPRs extending their reach: prokaryotic RNAi protein Cas9 recruited for gene regulation. EMBO J 32: 1802-1804.

    Heidrich, N., Vogel, J. (2013) Same Same but Different: New Structural Insight into CRISPR‐Cas Complexes. Mol Cell, 52, 4–7.

    Hein S, Scholz I, Voss B, Hess WR (2013) Adaptation and modification of three CRISPR loci in two closely related cyanobacteria. RNA Biol 10: 852-864.

    Hrle, A., Su, A.A.H., Ebert, J., Benda, C., Randau, L. and Conti, E. (2013) Structure and RNA-binding properties of the Type III-A CRISPR-associated protein Csm3. RNA Biol, 41: 1459-1463 (joint first and corresponding authorship).

    Jaubert, C., Danioux, C., Oberto, J., Cortez, D., Bize, A., Krupovic, M., She, Q., Forterre, P., Prangishvili, D., and Sezonov, G. (2013) Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon. Open Biol. 3, 130010.

    Kenchappa CS, Heidarsson PO, Kragelund BB, Garrett RA, Poulsen FM (2013) Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2. Nucleic Acids Res 41: 3424-3435.

    Kopfmann S, Hess WR (2013) Toxin-antitoxin systems on the large defense plasmid pSYSA of Synechocystis sp. PCC 6803. J Biol Chem 288: 7399-7409.

    Lange SJ, Alkhnbashi O, Rose D, Will S, and Backofen R (2013) CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res, 41: 8034-44.

    Marchfelder A. (2013) A Sophisticated Defense System: CRISPR-Cas. RNA Biology 10: 655 - 658.

    Marchfelder, A, Maier, L.-K., Heidrich, N., Pul, Ü. (2013) CRISPR-Cas: das Immunsystem der Prokaryoten. Biologie in unserer Zeit, 43: 158-165.

    Maier LK, Lange SJ, Stoll B, Haas KA, Fischer S, Fischer E, Duchardt-Ferner E, Wöhnert J, Backofen R, Marchfelder A (2013) Essential requirements for the detection and degradation of invaders by the Haloferax volcanii CRISPR/Cas system I-B. RNA Biol 10: 865-874.

    Maier LK, Stoll B, Brendel J, Fischer S, Pfeiffer F, Dyall-Smith M, Marchfelder A (2013) The ring of confidence: a haloarchaeal CRISPR/Cas system. Biochem Soc Trans 41: 374-378.

    Mojica, F.J.M., Garrett, R.A. (2013) Discovery and seminal developments in the CRISPR field. In: CRISPR-Cas Systems (eds. Barrangou R., van der Oost, J) Springer Press, pp. 1-31.

    Nickel L, Weidenbach K, Jager D, Backofen R, Lange SJ, Heidrich N, Schmitz RA (2013) Two CRISPR-Cas systems in Methanosarcina mazei strain Go1 display common processing features despite belonging to different types I and III. RNA Biol 10: 779-791.

    Okutan E, Deng L, Mirlashari S, Uldahl K, Halim M, Liu C, Garrett RA, She Q, Peng X (2013) Novel insights into gene regulation of the rudivirus SIRV2 infecting Sulfolobus cells. RNA Biol 10: 875-885.

    Peng W, Li H, Hallstrom S, Peng N, Liang YX, She Q (2013) Genetic determinants of PAM-dependent DNA targeting and pre-crRNA processing in Sulfolobus islandicus. RNA Biol 10: 738-748.

    Ren,Y. Q. She, L. Huang (2013) Transcriptomic analysis of the SSV2 infection of Sulfolobus solfataricus with and without the integrative plasmid pSSVi. Virology 441,126-134.

    Richter H, Lange SJ, Backofen R, Randau L (2013) SF CRISPR: Comparative analysis of Cas6b processing and CRISPR RNA stability. RNA Biol 10: 700-707.

    Richter H, Mohr S, Randau L (2013) C/D box sRNA, CRISPR RNA and tRNA processing in an archaeon with a minimal fragmented genome. Biochem Soc Trans 41: 411-415.

    Richter, H., Randau, L. and Plagens, A. (2013) Exploiting CRISPR/Cas: Interference Mechanisms and Applications. Int J Mol Sci, 14: 14518-14531.

    Servin-Garciduenas, L.E., Peng, X., Garrett, R.A., Martinez-Romero, E. (2013) Genome sequence of a novel archaeal rudivirus recovered from a Mexican hot spring. Genome Ann. 1, e00040-12.

    Scholz I., Lange S.J., Hein, S., Hess W.R., Backofen R. (2013) CRISPR-Cas systems in the cyanobacterium Synechocystis sp. PCC6803 exhibit distinct processing pathways involving at least two Cas6 and a Cmr2 protein. PLoS ONE, 8(2), e56470.1- e56470.15.

    Shah SA, Erdmann S, Mojica FJ, Garrett RA (2013) Protospacer recognition motifs: Mixed identities and functional diversity. RNA Biol 10: 891-899.

    Stoll, B.,  Maier, L.-K., Lange, S. J., Brendel, J., Fischer, S., Backofen, R. and Marchfelder, A. (2013) Requirements for a successful defence reaction by the CRISPR/Cas type I-B system. Biochem. Soc. Trans., 41: 1444-1448.

    Su AA, Tripp V, Randau L (2013) RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri. Nucleic Acids Res 41: 6250-6258.

    Zhang Y*, Heidrich N*, Ampattu BJ, Gunderson CW, Seifert HS, Schoen C, Vogel J, Sontheimer EJ (2013) Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis. Mol Cell 50: 488-503.

    *These authors contributed equally to this work.

    Zöphel, J and Randau, L. (2013) RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns. Biochem Soc Trans, 41, 1459-1463.

  • 2012

    Deng L, Kenchappa CS, Peng X, She Q, Garrett RA. (2012) Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus. Nucleic Acids Res. 40:2470-80.

    Ellinger P, Arslan Z, Wurm R, Tschapek B, Mackenzie C, Pfeffer K, Panjikar S, Wagner R, Schmitt L, Gohlke H, Pul Ü, Smits SH. (2012) The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae. J Struct Biol. 178:350-62.

    Erdmann S, Garrett RA. (2012) Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms. Mol Microbiol. 85: 1044-56.

    Fischer S, Maier LK, Stoll B, Brendel J, Fischer E, Pfeiffer F, Dyall-Smith M, Marchfelder A. (2012) An archaeal immune system can detect multiple protospacer adjacent motifs (PAMs) to target invader DNA. J Biol Chem. 287: 33351-65

    Maier, L. K., Fischer, S., Stoll, B., Brendel, J., Pfeiffer, F., Dyall-Smith, M., and Marchfelder, A. (2012) The immune system of halophilic archaea. Mob Genet Elements. 2, 228-232.

    Marchfelder A, Fischer S, Brendel J, Stoll B, Maier LK, Jäger D, Prasse D, Plagens A, Schmitz RA, Randau L. (2012) Small RNAs for defence and regulation in archaea. Extremophiles. 16: 685-696

    Peng X, Garrett RA, She Q. (2012) Archaeal viruses-novel, diverse and enigmatic. Sci China Life Sci. 55:422-33.

    Plagens A, Tjaden B, Hagemann A, Randau L, Hensel R. (2012) Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax. J Bacteriol. 194: 2491-500.

    Randau, L. (2012) RNA processing in the minimal organism Nanoarchaeum equitans. Genome Biol, 13:R63.

    Richter, H., Zoephel, J., Schermuly, J., Maticzka, D., Backofen, R., and Randau, L. (2012) Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis. Nucleic Acids Res. 40, 9887-9896.

    Stratmann T, Pul Ü, Wurm R, Wagner R, Schnetz K. (2012) RcsB-BglJ activates the Escherichia coli leuO gene, encoding an H-NS antagonist and pleiotropic regulator of virulence determinants. Mol Microbiol. 83:1109-23.

    Trautmann D., Voß B., Wilde A., Al-Babili S., Hess W.R (2012) Microevolution in cyanobacteria: Re-sequencing a motile substrain of Synechocystis sp. PCC 6803. DNA Research 19, 435-448.

    Wagner R, Pul Ü (2012) CRISPR - a bacterial immunity system based on small RNAs In: From Nucleic Acids Sequences to Molecular Medicine, Erdmann, Volker A.; Barciszewski, Jan (Eds.), Springer-Verlag IX, 121-143

    Zoephel J, Dwarakanath S, Richter H, Plagens A, Randau L (2012) Substrate generation for endonucleases of CRISPR/cas systems. J Vis Exp 67, 4277.

  • Before 2012

    Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471(7340): 602-607.

    Garrett RA, Shah SA, Vestergaard G, Deng L, Gudbergsdottir S, Kenchappa CS, Erdmann S, She Q (2011) CRISPR-based immune systems of the Sulfolobales: complexity and diversity. Biochem 39(1): 51-57.

    Garrett RA, Vestergaard G, Shah SA (2011) Archaeal CRISPR-based immune systems: exchangeable functional modules. Trends Microbiol 19(11): 549-556. Epub 2011 Sep 2022.

    Gudbergsdottir S, Deng L, Chen Z, Jensen JV, Jensen LR, She Q, Garrett RA (2011) Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers. Mol Microbiol 79(1): 35-49

    Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul Ü, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ (2011) Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol  18(5): 529-536.

    Shah SA, Garrett RA (2011) CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems. Res Microbiol 162(1): 27-38.

    You XY, Liu C, Wang SY, Jiang CY, Shah SA, Prangishvili D, She Q, Liu SJ, Garrett RA (2011) Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles. Extremophiles 15(4): 487-497

    Pul Ü, Wurm R, Arslan Z, Geissen R, Hofmann N, Wagner R (2010) Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS. Mol Microbiol 75(6): 1495-1512

    Westra ER, Pul Ü, Heidrich N, Jore MM, Lundgren M, Stratmann T, Wurm R, Raine A, Mescher M, Van Heereveld L, Mastop M, Wagner EG, Schnetz K, Van Der Oost J, Wagner R, Brouns SJ (2010) H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO. Mol Microbiol 77(6): 1380-1393

    Lillestøl RK, Shah SA, Brugger K, Redder P, Phan H, Christiansen J, Garrett RA (2009) CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol Microbiol 72(1): 259-272

    Shah SA, Hansen NR, Garrett RA (2009) Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism. Biochem Soc Trans 37(Pt 1): 23-28.

    Vestergaard G, Shah SA, Bize A, Reitberger W, Reuter M, Phan H, Briegel A, Rachel R, Garrett RA, Prangishvili D (2008) Stygiolobus rod-shaped virus and the interplay of crenarchaeal rudiviruses with the CRISPR antiviral system. J Bacteriol 190(20): 6837-6845. Epub 2008 Aug 6822.

    Lillestøl RK, Redder P, Garrett RA, Brugger K (2006) A putative viral defence mechanism in archaeal cells. Archaea 2(1): 59-72.

    Prangishvili D, Forterre P, Garrett RA (2006) Viruses of the Archaea: a unifying view. Nat Rev Microbiol 4(11): 837-848.

    Prangishvili D, Garrett RA, Koonin EV (2006) Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res 117(1): 52-67. Epub 2006 Feb 2028.

    Prangishvili D, Garrett RA (2005) Viruses of hyperthermophilic Crenarchaea. Trends Microbiol 13(11): 535-542. Epub 2005 Sep 2008.

    Greve B, Jensen S, Brugger K, Zillig W, Garrett RA (2004) Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea 1(4): 231-239.

    Peng X, Brugger K, Shen B, Chen L, She Q, Garrett RA (2003) Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes. J Bacteriol 185(8): 2410-2417.

    She Q, Peng X, Zillig W, Garrett RA (2001) Gene capture in archaeal chromosomes. Nature 409(6819): 478.

Publications

Last update: November 2016

List of publications

  • 2016

    Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system. Gleditzsch D, Müller-Esparza H, Pausch P, Sharma K, Dwarakanath S, Urlaub H, Bange G, Randau L. Nucleic Acids Res. 2016  44: 5872-82.

    A Non-Stem-Loop CRISPR RNA Is Processed by Dual Binding Cas6. Shao Y, Richter H, Sun S, Sharma K, Urlaub H, Randau L, Li H. Structure. 2016 24:547-54.

    Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs. Reimann V, Alkhnbashi OS, Saunders SJ, Scholz I, Hein S, Backofen R, Hess WR. Nucleic Acids Res. 2016 Sep 5. pii: gkw786. [Epub ahead of print]

    Characterizing leader sequences of CRISPR loci. Alkhnbashi OS, Shah SA, Garrett RA, Saunders SJ, Costa F, Backofen R. Bioinformatics. 2016 32:i 576-i585.

    Gene Repression in Haloarchaea Using the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas I-B System. Stachler AE, Marchfelder A. J Biol Chem. 2016 291: 15226-42.

    Engineering of temperature- and light-switchable Cas9 variants. Richter F, Fonfara I, Bouazza B, Schumacher CH, Bratovič M, Charpentier E, Möglich A. Nucleic Acids Res. 2016 Oct 15. pii: gkw930. [Epub ahead of print]

    CRISPR-Cas: biology, mechanisms and relevance. Hille F, Charpentier E. Philos Trans R Soc Lond B Biol Sci. 2016 371(1707).

    The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E. Nature. 2016 532: 517-21.

    Adaptation in CRISPR-Cas Systems. Sternberg SH, Richter H, Charpentier E, Qimron U. Mol Cell. 2016 61: 797-808.

    Major and minor crRNA annealing sites facilitate low stringency DNA protospacer binding prior to Type I-A CRISPR-Cas interference in Sulfolobus. Mousaei M, Deng L, She Q, Garrett RA. RNA Biol. 2016 13: 1166-1173.

    Diverse CRISPR-Cas responses and dramatic cellular DNA changes and cell death in pKEF9-conjugated Sulfolobus species. Liu G, She Q, Garrett RA. Nucleic Acids Res. 2016 44: 4233-42.

    Transcriptome changes in STSV2-infected Sulfolobus islandicus REY15A undergoing continuous CRISPR spacer acquisition. León-Sobrino C, Kot WP, Garrett RA. Mol Microbiol. 2016 99:719-28.

    Harnessing Type I and Type III CRISPR-Cas systems for genome editing. Li Y, Pan S, Zhang Y, Ren M, Feng M, Peng N, Chen L, Liang YX, She Q. Nucleic Acids Res. 2016 44: e34.

  • 2015

    Toward Whole-Transcriptome Editing with CRISPR-Cas9. Heckl D, Charpentier E. Mol Cell. 2015 58: 560-2.

    Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. Charpentier E, Richter H, van der Oost J, White MF. FEMS Microbiol Rev. 2015 39: 428-41.

    CRISPR germline engineering--the community speaks. Bosley KS, Botchan M, Bredenoord AL, Carroll D, Charo RA, Charpentier E, Cohen R, Corn J, Doudna J, Feng G, Greely HT, Isasi R, Ji W, Kim JS, Knoppers B, Lanphier E, Li J, Lovell-Badge R, Martin GS, Moreno J, Naldini L, Pera M, Perry AC, Venter JC, Zhang F, Zhou Q. Nat Biotechnol. 2015 33: 478-86.

    DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes. Plagens A, Richter H, Charpentier E, Randau L. FEMS Microbiol Rev. 2015 39: 442-63.

    CRISPR-Cas9: how research on a bacterial RNA-guided mechanism opened new perspectives in biotechnology and biomedicine. Charpentier E. EMBO Mol Med. 2015 7: 363-5.

    An updated evolutionary classification of CRISPR-Cas systems. Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV. Nat Rev Microbiol. 2015 13: 722-36.

    Interference activity of a minimal Type I CRISPR-Cas system from Shewanella putrefaciens. Dwarakanath S, Brenzinger S, Gleditzsch D, Plagens A, Klingl A, Thormann K, Randau L. Nucleic Acids Res. 2015 43: 8913-23.

    Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RH, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H. Methods. 2015 89: 138-48.

    In Vitro Co-reconstitution of Cas Protein Complexes. Plagens A, Randau L. Methods Mol Biol. 2015 1311: 23-33.

    DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes. Plagens A, Richter H, Charpentier E, Randau L. FEMS Microbiol Rev. 2015 39: 442-63.

    The role of Cas8 in type I CRISPR interference. Cass SD, Haas KA, Stoll B, Alkhnbashi OS, Sharma K, Urlaub H, Backofen R, Marchfelder A, Bolt EL. Biosci Rep. 2015 35(3).

    Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RH, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H. Methods. 2015 89: 138-48.

    The Adaptive Immune System of Haloferax volcanii. Maier LK, Dyall-Smith M, Marchfelder A. Life (Basel). 2015 5: 521-37.

    An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein. Maier LK, Stachler AE, Saunders SJ, Backofen R, Marchfelder A. J Biol Chem. 2015 290: 4192-201.

    Investigating CRISPR RNA Biogenesis and Function Using RNA-seq. Heidrich N1, Dugar G, Vogel J, Sharma CM. Methods Mol Biol. 2015 1311: 1-21.

    Archaeal Viruses of the Sulfolobales: Isolation, Infection, and CRISPR Spacer Acquisition. Erdmann S, Garrett RA. Methods Mol Biol. 2015 1311: 223-32.

    CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity. Garrett RA, Shah SA, Erdmann S, Liu G, Mousaei M, León-Sobrino C, Peng W, Gudbergsdottir S, Deng L, Vestergaard G, Peng X, She Q. Life (Basel). 2015 5: 783-817.

    Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR-Cas system.Fusco S, Liguori R, Limauro D, Bartolucci S, She Q, Contursi P. Biochimie. 2015 118: 322-32.

    Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition. Liu T, Li Y, Wang X, Ye Q, Li H, Liang Y, She Q, Peng N. Nucleic Acids Res. 2015 43: 1044-55.

    An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference. Peng W, Feng M, Feng X, Liang YX, She Q. Nucleic Acids Res. 2015 43: 406-17.

  • 2014

    Alkhnbashi OS, Costa F, Shah SA, Garrett RA, Saunders SJ, Backofen R. (2014) CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Bioinformatics. 2014 30:i489-96. doi: 10.1093/bioinformatics/btu459.

    Arslan Z*, Hermanns V*, Wurm R, Wagner R, Pul, Ü (2014) Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system, Nucl Acids Res, 42: 7884-93.

    *These authors contributed equally to this work.

    Benda C, Ebert J, Scheltema RA, Schiller HB, Baumgärtner M, Bonneau F, Mann M, Conti E. (2014) Structural model of a CRISPR RNA-silencing complex reveals the RNA-target cleavage activity in Cmr4. Mol Cell. 56:43-54. doi: 10.1016/j.molcel.2014.09.002.

    Brendel, J., Stoll, B., Lange, S.J., Stachler, A.-E., Maier, L.-K., Sharma, K., Richter ,H., Nickel, L., Schmitz, R.A., Randau, L., Urlaub, H., Allers, T., Backofen, R. and Marchfelder, A. (2014) Cas6 is necessary but not sufficient for a stable crRNA population in Haloferax volcanii, J Biol Chem, 289: 7164-7177.

    Daume M, Plagens A, Randau L. (2014) DNA binding properties of the small cascade subunit Csa5. PLoS One. 2014 9:e105716. doi: 10.1371/journal.pone.0105716. eCollection 2014.

    Erdmann S, Le Moine Bauer S, Garrett RA. (2014) Inter-viral conflicts that exploit host CRISPR immune systems of Sulfolobus. Mol Microbiol: 91:900-17.

    Heidrich N, Dugar G, Vogel J & Sharma CM (2014) Investigating CRISPR RNA biogenesis and function using RNA-seq. In: CRISPR Methods & Protocols, Charpentier E, Lundgren M, (Eds.), Springer Science + Business Media, LLC, in press.

    Hrle A, Maier LK, Sharma K, Ebert J, Basquin C, Urlaub H, Marchfelder A, Conti E. (2014) Structural analyses of the CRISPR protein Csc2 reveal the RNA-binding interface of the type I-D Cas7 family. RNA Biol. 11:1072-82. doi: 10.4161/rna.29893.

    Plagens, A., Tripp, V., Daume, M., Sharma, K., Klingl, A., Hrle, A., Conti, E., Urlaub, H. and Randau, L. (2014) In vitro assembly and activity of an archaeal CRISPR-Cas type I-A Cascade interference complex. Nucl Acids Res, 42: 5125-38.

    Plagens, A. and Randau, L. (2014) Small RNA-guided adaptive immunity: Comment on “Diversity, Evolution, and Therapeutic Applications of small RNAs in Prokaryotic and Eukaryotic Immune Systems” by Cooper and Overstreet. Phys. Life Rev. 11: 139-140.

    Plagens, A and Randau, L. (2014) In vitro co-reconstitution of Cas protein complexes. Meth Mol Biol, in press.

    Pul Ü (2014) Chemical and enzymatic footprint analyses of R-Loop formation by Cascade-crRNA complex. Meth Mol Biol, in press.

    Staals RH, Zhu Y, Taylor DW, Kornfeld JE, Sharma K, Barendregt A, Koehorst JJ, Vlot M, Neupane N, Varossieau K, Sakamoto K, Suzuki T, Dohmae N, Yokoyama S, Schaap PJ, Urlaub H, Heck AJ, Nogales E, Doudna JA, Shinkai A, van der Oost J. (2014) RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus. Mol Cell. 56:518-30. doi: 10.1016/j.molcel.2014.10.005. Epub 2014 Nov 6.

    Vestergaard, G., Garrett, R. A., and Shah, S. A. (2014) CRISPR adaptive immune systems of Archaea. RNA Biol. 11, 156-167.

  • 2013

    Arslan Z, Stratmann T, Wurm R, Wagner R, Schnetz K, Pul Ü (2013) RcsB-BglJ-mediated activation of Cascade operon does not induce the maturation of CRISPR RNAs in E. coli K12. RNA Biol 10: 708-715.

    Arslan Z, Wurm R, Brener O, Ellinger P, Nagel-Steger L, Oesterhelt F, Schmitt L, Willbold D, Wagner R, Gohlke H, Smits S, Pul Ü (2013) Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2. Nucl Acids Res 41: 6347-6359.

    Arslan Z, Westra ER, Wagner R, Pul Ü (2013) Regulation of CRISPR-based immune responses. In: CRISPR-Cas systems: RNA-mediated Adaptive Immunity in Bacteria and Archaea, Barrangou, Rodolphe; van der Oost, John (Eds.), Springer-Verlag X, 93-113.

    Deng L, Garrett RA, Shah SA, Peng X, She Q (2013) A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol Microbiol 87: 1088-1099.

    Dugar, G., Herbig, A., Förstner, K. U., Heidrich, N., Reinhardt, R., Nieselt, K., Sharma, C. M. (2013) High‐Resolution Transcriptome Maps Reveal Strain‐Specific Regulatory Features of Multiple Campylobacter jejuni Isolates. PLoS Genetics, 9(5), e1003495.

    Erdmann, S., S.A. Shah, and R.A. Garrett (2013) SMV1 virus-induced CRISPR spacer acquisition from the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2. Biochem Soc Trans 41, 1449-1458.

    Erdmann, S., B. Chen, X. Huang, L. Deng, C. Liu, S.A. Shah, S.L.M. Bauer, C.L. Sobrino, H. Wang, Y. Wei, Q. She, R.A. Garrett, L. Huang, L. Lin (2013) A novel single-tailed fusiform Sulfolobus virus STSV2 infecting model Sulfolobus species. Extremophiles, in press.

    Fusco,S., Q. She, S. Bartolucci, P. Contursi (2013) Tlys, a novel identified SSV1 transcript expressed in the lysogenic state, encodes for a DNA-binding protein interacting at the promotersof the early genes. J Virol. 87, 5926-5936.

    Heidrich, N., Vogel J (2013) CRISPRs extending their reach: prokaryotic RNAi protein Cas9 recruited for gene regulation. EMBO J 32: 1802-1804.

    Heidrich, N., Vogel, J. (2013) Same Same but Different: New Structural Insight into CRISPR‐Cas Complexes. Mol Cell, 52, 4–7.

    Hein S, Scholz I, Voss B, Hess WR (2013) Adaptation and modification of three CRISPR loci in two closely related cyanobacteria. RNA Biol 10: 852-864.

    Hrle, A., Su, A.A.H., Ebert, J., Benda, C., Randau, L. and Conti, E. (2013) Structure and RNA-binding properties of the Type III-A CRISPR-associated protein Csm3. RNA Biol, 41: 1459-1463 (joint first and corresponding authorship).

    Jaubert, C., Danioux, C., Oberto, J., Cortez, D., Bize, A., Krupovic, M., She, Q., Forterre, P., Prangishvili, D., and Sezonov, G. (2013) Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon. Open Biol. 3, 130010.

    Kenchappa CS, Heidarsson PO, Kragelund BB, Garrett RA, Poulsen FM (2013) Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2. Nucleic Acids Res 41: 3424-3435.

    Kopfmann S, Hess WR (2013) Toxin-antitoxin systems on the large defense plasmid pSYSA of Synechocystis sp. PCC 6803. J Biol Chem 288: 7399-7409.

    Lange SJ, Alkhnbashi O, Rose D, Will S, and Backofen R (2013) CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res, 41: 8034-44.

    Marchfelder A. (2013) A Sophisticated Defense System: CRISPR-Cas. RNA Biology 10: 655 - 658.

    Marchfelder, A, Maier, L.-K., Heidrich, N., Pul, Ü. (2013) CRISPR-Cas: das Immunsystem der Prokaryoten. Biologie in unserer Zeit, 43: 158-165.

    Maier LK, Lange SJ, Stoll B, Haas KA, Fischer S, Fischer E, Duchardt-Ferner E, Wöhnert J, Backofen R, Marchfelder A (2013) Essential requirements for the detection and degradation of invaders by the Haloferax volcanii CRISPR/Cas system I-B. RNA Biol 10: 865-874.

    Maier LK, Stoll B, Brendel J, Fischer S, Pfeiffer F, Dyall-Smith M, Marchfelder A (2013) The ring of confidence: a haloarchaeal CRISPR/Cas system. Biochem Soc Trans 41: 374-378.

    Mojica, F.J.M., Garrett, R.A. (2013) Discovery and seminal developments in the CRISPR field. In: CRISPR-Cas Systems (eds. Barrangou R., van der Oost, J) Springer Press, pp. 1-31.

    Nickel L, Weidenbach K, Jager D, Backofen R, Lange SJ, Heidrich N, Schmitz RA (2013) Two CRISPR-Cas systems in Methanosarcina mazei strain Go1 display common processing features despite belonging to different types I and III. RNA Biol 10: 779-791.

    Okutan E, Deng L, Mirlashari S, Uldahl K, Halim M, Liu C, Garrett RA, She Q, Peng X (2013) Novel insights into gene regulation of the rudivirus SIRV2 infecting Sulfolobus cells. RNA Biol 10: 875-885.

    Peng W, Li H, Hallstrom S, Peng N, Liang YX, She Q (2013) Genetic determinants of PAM-dependent DNA targeting and pre-crRNA processing in Sulfolobus islandicus. RNA Biol 10: 738-748.

    Ren,Y. Q. She, L. Huang (2013) Transcriptomic analysis of the SSV2 infection of Sulfolobus solfataricus with and without the integrative plasmid pSSVi. Virology 441,126-134.

    Richter H, Lange SJ, Backofen R, Randau L (2013) SF CRISPR: Comparative analysis of Cas6b processing and CRISPR RNA stability. RNA Biol 10: 700-707.

    Richter H, Mohr S, Randau L (2013) C/D box sRNA, CRISPR RNA and tRNA processing in an archaeon with a minimal fragmented genome. Biochem Soc Trans 41: 411-415.

    Richter, H., Randau, L. and Plagens, A. (2013) Exploiting CRISPR/Cas: Interference Mechanisms and Applications. Int J Mol Sci, 14: 14518-14531.

    Servin-Garciduenas, L.E., Peng, X., Garrett, R.A., Martinez-Romero, E. (2013) Genome sequence of a novel archaeal rudivirus recovered from a Mexican hot spring. Genome Ann. 1, e00040-12.

    Scholz I., Lange S.J., Hein, S., Hess W.R., Backofen R. (2013) CRISPR-Cas systems in the cyanobacterium Synechocystis sp. PCC6803 exhibit distinct processing pathways involving at least two Cas6 and a Cmr2 protein. PLoS ONE, 8(2), e56470.1- e56470.15.

    Shah SA, Erdmann S, Mojica FJ, Garrett RA (2013) Protospacer recognition motifs: Mixed identities and functional diversity. RNA Biol 10: 891-899.

    Stoll, B.,  Maier, L.-K., Lange, S. J., Brendel, J., Fischer, S., Backofen, R. and Marchfelder, A. (2013) Requirements for a successful defence reaction by the CRISPR/Cas type I-B system. Biochem. Soc. Trans., 41: 1444-1448.

    Su AA, Tripp V, Randau L (2013) RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri. Nucleic Acids Res 41: 6250-6258.

    Zhang Y*, Heidrich N*, Ampattu BJ, Gunderson CW, Seifert HS, Schoen C, Vogel J, Sontheimer EJ (2013) Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis. Mol Cell 50: 488-503.

    *These authors contributed equally to this work.

    Zöphel, J and Randau, L. (2013) RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns. Biochem Soc Trans, 41, 1459-1463.

  • 2012

    Deng L, Kenchappa CS, Peng X, She Q, Garrett RA. (2012) Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus. Nucleic Acids Res. 40:2470-80.

    Ellinger P, Arslan Z, Wurm R, Tschapek B, Mackenzie C, Pfeffer K, Panjikar S, Wagner R, Schmitt L, Gohlke H, Pul Ü, Smits SH. (2012) The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae. J Struct Biol. 178:350-62.

    Erdmann S, Garrett RA. (2012) Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms. Mol Microbiol. 85: 1044-56.

    Fischer S, Maier LK, Stoll B, Brendel J, Fischer E, Pfeiffer F, Dyall-Smith M, Marchfelder A. (2012) An archaeal immune system can detect multiple protospacer adjacent motifs (PAMs) to target invader DNA. J Biol Chem. 287: 33351-65

    Maier, L. K., Fischer, S., Stoll, B., Brendel, J., Pfeiffer, F., Dyall-Smith, M., and Marchfelder, A. (2012) The immune system of halophilic archaea. Mob Genet Elements. 2, 228-232.

    Marchfelder A, Fischer S, Brendel J, Stoll B, Maier LK, Jäger D, Prasse D, Plagens A, Schmitz RA, Randau L. (2012) Small RNAs for defence and regulation in archaea. Extremophiles. 16: 685-696

    Peng X, Garrett RA, She Q. (2012) Archaeal viruses-novel, diverse and enigmatic. Sci China Life Sci. 55:422-33.

    Plagens A, Tjaden B, Hagemann A, Randau L, Hensel R. (2012) Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax. J Bacteriol. 194: 2491-500.

    Randau, L. (2012) RNA processing in the minimal organism Nanoarchaeum equitans. Genome Biol, 13:R63.

    Richter, H., Zoephel, J., Schermuly, J., Maticzka, D., Backofen, R., and Randau, L. (2012) Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis. Nucleic Acids Res. 40, 9887-9896.

    Stratmann T, Pul Ü, Wurm R, Wagner R, Schnetz K. (2012) RcsB-BglJ activates the Escherichia coli leuO gene, encoding an H-NS antagonist and pleiotropic regulator of virulence determinants. Mol Microbiol. 83:1109-23.

    Trautmann D., Voß B., Wilde A., Al-Babili S., Hess W.R (2012) Microevolution in cyanobacteria: Re-sequencing a motile substrain of Synechocystis sp. PCC 6803. DNA Research 19, 435-448.

    Wagner R, Pul Ü (2012) CRISPR - a bacterial immunity system based on small RNAs In: From Nucleic Acids Sequences to Molecular Medicine, Erdmann, Volker A.; Barciszewski, Jan (Eds.), Springer-Verlag IX, 121-143

    Zoephel J, Dwarakanath S, Richter H, Plagens A, Randau L (2012) Substrate generation for endonucleases of CRISPR/cas systems. J Vis Exp 67, 4277.

  • Before 2012

    Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471(7340): 602-607.

    Garrett RA, Shah SA, Vestergaard G, Deng L, Gudbergsdottir S, Kenchappa CS, Erdmann S, She Q (2011) CRISPR-based immune systems of the Sulfolobales: complexity and diversity. Biochem 39(1): 51-57.

    Garrett RA, Vestergaard G, Shah SA (2011) Archaeal CRISPR-based immune systems: exchangeable functional modules. Trends Microbiol 19(11): 549-556. Epub 2011 Sep 2022.

    Gudbergsdottir S, Deng L, Chen Z, Jensen JV, Jensen LR, She Q, Garrett RA (2011) Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers. Mol Microbiol 79(1): 35-49

    Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul Ü, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ (2011) Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol  18(5): 529-536.

    Shah SA, Garrett RA (2011) CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems. Res Microbiol 162(1): 27-38.

    You XY, Liu C, Wang SY, Jiang CY, Shah SA, Prangishvili D, She Q, Liu SJ, Garrett RA (2011) Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles. Extremophiles 15(4): 487-497

    Pul Ü, Wurm R, Arslan Z, Geissen R, Hofmann N, Wagner R (2010) Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS. Mol Microbiol 75(6): 1495-1512

    Westra ER, Pul Ü, Heidrich N, Jore MM, Lundgren M, Stratmann T, Wurm R, Raine A, Mescher M, Van Heereveld L, Mastop M, Wagner EG, Schnetz K, Van Der Oost J, Wagner R, Brouns SJ (2010) H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO. Mol Microbiol 77(6): 1380-1393

    Lillestøl RK, Shah SA, Brugger K, Redder P, Phan H, Christiansen J, Garrett RA (2009) CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol Microbiol 72(1): 259-272

    Shah SA, Hansen NR, Garrett RA (2009) Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism. Biochem Soc Trans 37(Pt 1): 23-28.

    Vestergaard G, Shah SA, Bize A, Reitberger W, Reuter M, Phan H, Briegel A, Rachel R, Garrett RA, Prangishvili D (2008) Stygiolobus rod-shaped virus and the interplay of crenarchaeal rudiviruses with the CRISPR antiviral system. J Bacteriol 190(20): 6837-6845. Epub 2008 Aug 6822.

    Lillestøl RK, Redder P, Garrett RA, Brugger K (2006) A putative viral defence mechanism in archaeal cells. Archaea 2(1): 59-72.

    Prangishvili D, Forterre P, Garrett RA (2006) Viruses of the Archaea: a unifying view. Nat Rev Microbiol 4(11): 837-848.

    Prangishvili D, Garrett RA, Koonin EV (2006) Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res 117(1): 52-67. Epub 2006 Feb 2028.

    Prangishvili D, Garrett RA (2005) Viruses of hyperthermophilic Crenarchaea. Trends Microbiol 13(11): 535-542. Epub 2005 Sep 2008.

    Greve B, Jensen S, Brugger K, Zillig W, Garrett RA (2004) Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea 1(4): 231-239.

    Peng X, Brugger K, Shen B, Chen L, She Q, Garrett RA (2003) Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes. J Bacteriol 185(8): 2410-2417.

    She Q, Peng X, Zillig W, Garrett RA (2001) Gene capture in archaeal chromosomes. Nature 409(6819): 478.

Contact

Coordinator:

Prof. Dr. Anita Marchfelder
Biology II
Ulm University
89069 Ulm
Phone: +49 - 731-50-22658
Fax:      +49 - 731-50-12-22658
anita.marchfelder(at)uni-ulm.de

Secretary:

Annemarie Windeck
Phone: +49 - 731-50-23931
Fax:      +49 - 731-50-23932
annemarie.windeck(at)uni-ulm.de