Publications – University of Copenhagen

Forward this page to a friend Resize Print Bookmark and Share

DAC > Publications

Publications

2016

12. Martinez Alvarez, Laura; Bell, Stephen; Peng, Xu. 2016. Multiple consecutive initiation of replication producing novel brush-like intermediates at the termini of linear viral dsDNA genomes with hairpin ends. Nucleic Acids Research, Vol. 44, nr. 18, s. 8799-8809.

11. Garrett, Roger Antony.2016. Archaeal physiology: The secrets of termination. Nature Microbiology 2016 Sep 27;1(10):16159.

10. Mousaei, Marzieh; Deng, Ling; She, Qunxin; Garrett, Roger Antony. 2016. Major and minor crRNA annealing sites facilitate low stringency DNA protospacer binding prior to Type I-A CRISPR-Cas interference in Sulfolobus. RNA Biology, Vol. 13, nr. 11, s. 1166-1173.

9. Guannan, Liu; She, Qunxin; Garrett, Roger Antony.2016. Diverse CRISPR-Cas responses and dramatic cellular DNA changes and cell death in pKEF9-conjugated Sulfolobus species. Nucleic Acids Research, Vol. 44, Nr. 9, s. 4233-4242.

8. Li, Yingjun; Pan, Saifu; Zhang, Yan; Ren, Min; Feng, Mingxia; Peng, Nan; Chen, Lanming; Liang, Yun Xiang; She, Qunxin. 2016. Harnessing type I and type III CRISPR-Cas systems for genome editing. Nucleic acids research, Vol. 44, Nr. 4, e34, 2016.

7. Uldahl, Kristine Buch; Jensen, Signe B.; Bhoobalan-Chitty, Yuvaraj; Martinez Alvarez, Laura; Papathanasiou, Pavlos; Peng, Xu. 2016. Life cycle characterization of Sulfolobus monocaudavirus 1, an extremophilic spindle-shaped virus with extracellular tail development. Journal of Virology, Vol. 90, Nr. 12, s. 5693-5699.

6. León Sobrino, Carlos; Kot, W.P.; Garrett, Roger Antony. 2016. Transcriptome changes in STSV2-infected Sulfolobus islandicus REY15A undergoing continuous CRISPR spacer acquisition. Molecular Microbiology, Vol. 99, Nr. 4, s. 719-728.

5. Gavrilov, Sergey N.; Stracke, Christina; Jensen, Kenneth; Menzel, Peter; Kallnik, Verena; Slesarev, Alexei; Sokolova, Tatyana; Zayulina, Kseniya; Bräsen, Christopher; Bonch-Osmolovskaya, Elizaveta A.; Peng, Xu; Kublanov, Ilya V.; Siebers, Bettina. 2016. solation and characterization of the first Xylanolytic hyperthermophilic euryarchaeon Thermococcus sp strain 2319x1 and its unusual multidomain glycosidase. Frontiers in Microbiology, Vol. 7, 552, 2016.

4. Islin, Sóley Ruth; Menzel, Peter; Krogh, Anders; Young, Mark; Peng, Xu. 2016. Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs. Environmental Microbiology, Vol. 18, Nr. 3,  s. 863-874.

3. Zarafeta, Dimitra; Kissas, Dimitrios; Sayer, Christopher; Islin, Sóley Ruth; Ladoukakis, Efthymios; Isupov, Michail N.; Chatziioannou, Aristotelis; Peng, Xu; Littlechild, Jennifer A.; Skretas, Georgios; Kolisis, Fragiskos N.2016. Discovery and characterization of a thermostable and highly halotolerant GH5 cellulase from an Icelandic hot spring isolate. P L o S One, Vol. 11, Nr. 1, e0146454, 2016.

2. Lin, Jinzhong; Zou, Yexia; Ma, Chengjie; Liang, Yunxiang; Ge, Xiangyang; Chen, Zhengjun; She, Qunxin. 2016. Construction and characterization of three protein-targeting expression system in Lactobacillus casei. F E M S Microbiology Letters, Vol. 363, Nr. 7, 2016.

1. Zhang, Changyi; She, Qunxin; Bi, Hongkai; Whitaker, Rachel J. 2016 The apt/6-methylpurine counterselection system and its applications in genetic studies of the hyperthermophilic archaeon Sulfolobus islandicus. Applied and Environmental Microbiology, Vol. 82, Nr. 10, 2016, s. 3070-3081.

2015

14. 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. 2015. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 13(11):722-36.

13. Fusco S, Liguori R, Limauro D, Bartolucci S, She Q, Contursi P. 2015. Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR-Cas system. Biochimie. 118:322-332.

12. Fusco S, She Q, Fiorentino G, Bartolucci S, Contursi P. 2015. Unravelling the Role of the F55 Regulator in the Transition from Lysogeny to UV Induction of Sulfolobus Spindle-Shaped Virus 1. J Virol. 89(12):6453-61. doi: 10.1128/JVI.00363-15. Epub 2015 Apr 15.

11. Erdmann S, Garrett RA. 2015. Archaeal Viruses of the Sulfolobales: Isolation, Infection, and CRISPR Spacer Acquisition. Methods Mol Biol. 1311:223-32. doi: 10.1007/978-1-4939-2687-9_14.

10. Cerveau N, Gilbert C, Liu C, Garrett RA, Grève P, Bouchon D, Cordaux R. 2015. Genomic context drives transcription of insertion sequences in the bacterial endosymbiont Wolbachia wVulC. Gene 564(1):81-6. doi: 10.1016/j.gene.2015.03.044. Epub 2015 Mar 23.

9. Ferrandi EE, Sayer C, Isupov MN, Annovazzi C, Marchesi C, Iacobone G, Peng X, Bonch-Osmolovskaya E, Wohlgemuth R, Littlechild JA, Monti D. 2015. Discovery and characterization of thermophilic limonene-1,2-epoxide hydrolases from hot spring metagenomic libraries. FEBS J. 282(15):2879-94. doi: 10.1111/febs.13328. Epub 2015 Jun 16.

8. Guo Y, Kragelund BB, White MF, Peng X. 2015. Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities. J Mol Biol. 427(12):2179-2191.

7. Menzel P, Gudbergsdóttir SR, Rike AG, Lin L, Zhang Q, Contursi P, Moracci M, Kristjansson JK, Bolduc B, Gavrilov S, Ravin N, Mardanov A, Bonch-Osmolovskaya E, Young M, Krogh A, Peng X. 2015. Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs. Microb Ecol. 70(2):411-24.

6. R.A. Garrett, S.A. Shah, S. Erdmann, G. Liu, M. Mousaei, C. León-Sobrino, W. Peng, S. Gudbergsdottir, L. Deng, G. Vestergaard, X. Peng, Q. She. 2015. CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity. Life (Basel) 5(1):783-817.

5. Huang Q, Liu L, Liu J, Ni J, She Q, Shen Y. 2015. Efficient 5'-3' DNA end resection by HerA and NurA is essential for cell viability in the crenarchaeon Sulfolobus islandicus. BMC Mol Biol. 2015 Feb 14;16:2. doi: 10.1186/s12867-015-0030-z.

4. H. Wang, N. Peng, S. A. Shah, L. Huang, Q. She. 2015. Archaeal Extrachromosomal Genetic Elements. Microbiol Mol Biol Rev. 79(1):117-152.

3. Q. Huang, Y. Li, C. Zeng, T. Song, Z. Yan, Ni J, Q. She, Y. Shen. 2015. Genetic analysis of the Holliday junction resolvases Hje and Hjc in Sulfolobus islandicus. Extremophiles. 19(2):505-514. 

2. T. Liu, Y. Li, X. Wang, Q. Ye, H. Li, Y. Liang, Q. She, N. Peng. 2015. Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition. Nucleic Acids Res. 43(2):1044-55.

1. W. Peng, M. Feng, X. Feng, Y.X. Liang, Q. She. 2015. An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference. Nucleic Acids Res. 43(1):406-17. 

2014

14. Sun X, Liu T, Peng X, Chen L. 2014. Insights into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis. Int J Mol Sci. 15(12):22539-62. doi: 10.3390/ijms151222539.

13. F. He, L. Chen, X. Peng. 2014. First Experimental Evidence for the Presence of a CRISPR Toxin in Sulfolobus. J Mol Biol. 2014 Nov 11;426(22):3683-8. doi: 10.1016/j.jmb.2014.09.016. Epub 2014 Sep 30.

12. O.S. Alkhnbashi, F. Costa, S.A. Shah, R.A. Garrett, S.J. Saunders, R. Backofen. 2014. CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Bioinformatics. 2014 Sep 1;30(17):i489-96. doi: 10.1093/bioinformatics/btu459.

11. H. Jin, B. Li, X. Peng, L. Chen. 2014. Metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in Shanghai, China. Ann Microbiol 64 (2):689-697.

10. L. Deng, F. He, Y Bhoobalan-Chitty, L. Martinez-Alvarez, Y. Guo, Peng X. 2014. Unveiling cell surface and type IV secretion proteins responsible for archaeal rudivirus entry. J Virol 2014 Jun 25. pii: JVI.01495-14. [Epub ahead of print]

9. H. Han, Y. Shen, Q. She. Nanobiomotors of archaeal DNA repair machineries: current research status and application potential. Cell Biosci 2014 Jun 25;4:32. doi: 10.1186/2045-3701-4-32. eCollection 2014. Review.

8. L. J. Happonen, S. Erdmann, R. A. Garrett, S. J. Butcher. Adenosine Triphosphatases of Thermophilic Archaeal Double-stranded DNA Viruses. Cell Biosci 2014, Jul 23;4:37. doi: 10.1186/2045-3701-4-37. eCollection 2014. Review.

7. X. Xing, L. Zhang, L. Guo, Q. She, L. Huang. Sulfolobus replication factor C stimulates the activity of DNA polymerase B1. J Bacteriol 196: 2367-2375. Published ahead of print 18 April 2014, doi: 10.1128/JB.01552-14.

6. Z. Chen, J. Lin, C. Ma, S. Zhao, Q. She, Y. Liang. 2014. Characterization of pMC11, a plasmid with dual origins of replication isolated from Lactobacillus casei MCJ and construction of shuttle vectors with each replicon. Appl Microbiol Biotechnol 98(13):5977-89. doi: 10.1007/s00253-014-5649-z. Epub 2014 Mar 22.

5. R.A. Garrett. 2014. A backward view from 16S rRNA to archaea to the universal tree of life to progenotes: Reminiscences of Carl Woese. RNA Biol. 2014 Feb 26;11(3). [Epub ahead of print] Review.

4. P. Contursi, S. Fusco, R. Cannio, Q. She. 2014. Molecular biology of fuselloviruses and their satellites. Extremophiles. 2014 May;18(3):473-489.

3. G. Vestergaard, R.A. Garrett, S.A. Shah. 2014. CRISPR adaptive immune systems of Archaea. RNA Biol. 11(2):156-67.

2. S. Erdmann, S. Le Moine Bauer, R.A. Garrett. 2014. Inter-viral conflicts that exploit host CRISPR immune systems of Sulfolobus. Mol Microbiol. 91(5):900-917.

1. S. Erdmann, 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 18, 51-60.

2013

21. Erdmann S, Shah SA, Garrett RA. 2013. SMV1 virus-induced CRISPR spacer acquisition from the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2. Biochem Soc Trans. 41, 1449-58. doi: 10.1042/BST20130196

20. Y. Li, Y. Pan, Q. She, L. Chen. 2013. A novel carboxyl-terminal protease derived from Paenibacillus lautus CHN26 exhibiting high activities at multiple sites of substrates. BMC Biotechnol. 2013, 13:89 (25 October 2013)

19. P.-J. Liang, W. Han, Q. Huang, Y. Li, J. Ni, Q. She, Y. Shen. 2013. Knockouts of RecA-Like Proteins RadC1 and RadC2 Have Distinct Responses to DNA Damage Agents in Sulfolobus islandicus. J. Gen. Genom. 40, 553-542.

18. Servin-Garciduenas, L.E., X. Peng, R.A. Garrett, E. Martinez-Romero. 2013. Genome sequence of a novel archaeal fusellovirus assembled from the metagenome of a mexican hot spring. Genome Announc. 2013 Apr 25; 1(2):e0016413. doi: 10.1128/genomeA.00164-13. 

17. Jaubert C, Danioux C, Oberto J, Cortezn D, Bize A, Krupovic M, She Q, Forterre P, Prangishvili D and Sezonov G.  Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon. Open Biol.  2013 Apr 17; 3(4):130010. doi: 10.1098/rsob.130010

16.  Ren Y, She Q, Huang L. 2013. Transcriptomic analysis of the SSV2 infection of Sulfolobus solfataricus with and without the integrative plasmid pSSVi. Virology. 441, 126-134. doi:pii: S0042-6822(13)00152-9. 10.1016/j.virol.2013.03.012.

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

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

13. W. Peng, H. Li, S. Hallstrøm, N. Peng, Y. X. Liang, Q. She. 2013. Genetic determinants of PAM-dependent DNA targeting and pre-crRNA processing in Sulfolobus islandicus. RNA Biol. 10, 738-748.

12. Zhang T, Pan Y, Li B, Ou J, Zhang J, Chen Y , Peng X & Chen. L. 2013. Molecular cloning and antimicrobial activity of enterolysin A and helveticin J of bacteriolysins from metagenome of Chinese traditional fermented foodsFood Control, vol 31, nr. 2, s. 499-507.

11. Fusco S, She Q, Bartolucci S & Contursi P. 2013. Tlys, a novel, newly identified Sulfolobus spindle-shaped virus 1 transcript expressed in the lysogenic state, encodes a DNA-binding protein interacting at the promoters of the early genesJournal of Virology. 87, 5926-5936.

10. Shi Y, Pan Y, Li B, He W, She Q, Chen L. 2013. Molecular cloning of a novel bioH gene from an environmental metagenome encoding a carboxylesterase with exceptional tolerance to organic solvents. BMC Biotechnol. 2013 Feb 15;13:13. doi: 10.1186/1472-6750-13-13.

9. Servín-Garcidueñas LE, Peng X, Garrett RA, Martínez-Romero E. 2013. Genome sequence of a novel archaeal rudivirus recovered from a mexican hot spring. Genome Announc. 2013 Jan;1(1). doi:pii: e00040-12. 10.1128/genomeA.00040-12. Epub 2013 Jan 15.

8. Servín-Garcidueñas LE, Garrett RA, Amils R, Martínez-Romero E. 2013. Genome Sequence of the Acidophilic Bacterium Acidocella sp. Strain MX-AZ02. Genome Announc. 2013 Jan;1(1). doi:pii: e00041-12. 10.1128/genomeA.00041-12. Epub 2013 Jan 15.

7. 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. 2013 Mar 1;41(5):3424-35. doi: 10.1093/nar/gks1465.

6. L. Deng, R.A. Garrett, S.A. Shah, X. Peng*, Q. She*. 2013. A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol. Microbiol. 2013 March 87(5):1088-99. Full text

5. R.Y. Samson#, Y. Xu#, C. Gadelha, T.A. Stone, J.N. Faqiri, D. Li, N. Qin, F. Pu, Y.X. Liang, Q. She*, and S.D. Bell*.2013. Specificity and Function of Archaeal DNA Replication Initiator Proteins. Cell Reports 2013. Feb 21;3(2), 485-96. Full Text

4. Zhang C, Tian B, Li S, Ao X, Dalgaard K, Gökce S, Liang Y, She Q. 2013. Genetic manipulation in Sulfolobus islandicus and functional analysis of DNA repair genes. Biochem Soc Trans. 2013 Feb 1;41(1):405-10. doi: 10.1042/BST20120285.

3. Uldahl K, Peng X. 2013. Biology, biodiversity and application potential of thermophilic viruses, in  T. Satyanarayana et al. (eds.) “Thermophile Microbes in Environmental and Industrial Biotechnology: Biotechnology of Thermophiles”. Springer, s. 271-304.

2. Shah, SA & Garrett, RA 2013, ' Archaeal type II toxin-antitoxins '. i K Gerdes (red.), Prokaryotic toxin-antitoxins. Springer, s. 225-238.

1. Mojica, FJM & Garrett, RA 2013, ' Discovery and seminal developments in the CRISPR field '. i R Barrangou & J van der Oost (red), CRISPR-Cas Systems: RNA-mediated Adaptive Immunity in Bacteria and Archaea. Springer-VS, s. 1-31.

2012

10. Hu Y, Peng N, Han W, Mei Y, Chen Z, Feng X, Liang YX, She Q. An archaeal protein evolutionarily conserved in prokaryotes is a zinc-dependent metalloprotease. Biosci Rep. 2012 Dec;32(6):609-18. doi: 10.1042/BSR20120074.

9. Felisberto-Rodrigues C, Blangy S, Goulet A, Vestergaard G, Cambillau C, Garrett RA, Ortiz-Lombardía M. Crystal structure of ATV(ORF273), a new fold for a thermo- and acido-stable protein from the Acidianus two-tailed virus. PLoS One. 2012;7(10):e45847. doi: 10.1371/journal.pone.0045847. Epub 2012 Oct 8.

8. Erdmann S, Garrett RA. Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms. Mol Microbiol. 2012 Sep;85(6):1044-56.

 7. Peng N, Deng L, Mei Y, Jiang D, Hu Y, Awayez M, Liang Y, She Q. A synthetic arabinose-inducible promoter confers high levels of recombinant protein expression in hyperthermophilic archaeon Sulfolobus islandicus. Appl Environ Microbiol. 2012 Aug;78(16):5630-7. doi: 10.1128/AEM.00855-12. Epub 2012 Jun 1.

6. Peng X, Garrett RA, She Q. Archaeal viruses--novel, diverse and enigmatic. Sci China Life Sci. 2012 May;55(5):422-33. Epub 2012 May 27.

5. Pichon S, Bouchon D, Liu C, Chen L, Garrett RA, Greve P. The expression of one ankyrin pk2 allele of the WO prophage is correlated with the Wolbachia feminizing effect in isopods. BMC Microbiol. 2012 Apr 12;12(1):55. [Epub ahead of print] (2011) Abstract

4. Deng L, Kerchappa CS, Peng X, She Q*, Garrett RA*. Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus. Nucleic Acids Res. 2012 Mar;40(6):2470-80. doi: 10.1093/nar/gkr1111. Epub 2011 Dec 1.

3. Zheng T, Huang Q, Zhang C, Ni J, She Q*, Shen Y*. Development of a simvastatin selection marker for a hyperthermophilic acidophile, Sulfolobus islandicus. Appl Environ Microbiol. 2012 Jan;78(2):568-74. doi: 10.1128/AEM.06095-11. Epub 2011 Nov 11.

2. Hong Y, Chu M, Li Y, Ni J, Sheng D, Hou G, She Q*, Shen Y*. Dissection of the functional domains of an archaeal Holliday junction helicase. DNA Repair (Amst). 2012 Feb 1;11(2):102-11. doi: 10.1016/j.dnarep.2011.10.009. Epub 2011 Nov 6.

1. Mei Y, Peng N, Zhao S, Hu Y, Wang H, Liang Y, She Q. Exceptional thermal stability and organic solvent tolerance of an esterase expressed from a thermophilic host. Appl Microbiol Biotechnol. 2012 Mar;93(5):1965-74. doi: 10.1007/s00253-011-3504-z. Epub 2011 Aug 17.

2011

14. Li X, Guo L, Deng L, Feng D, Ren Y, Chu Y, She Q*, Huang L*. Deletion of the topoisomerase III gene in the hyperthermophilic archaeon Sulfolobus islandicus results in slow growth and defects in cell cycle control. J Genet Genomics. 2011 Jun 20;38(6):253-9. Epub 2011 May 11. Abstract

13. Erdmann S, Scheele U, Garrett RA. AAA ATPase p529 of Acidianus two-tailed virus ATV and host receptor recognition. Virology. 2011 Dec 5;421(1):61-6. Epub 2011 Oct 7. Abstract

12. Garrett RA, Vestergaard G, Shah SA. Archaeal CRISPR-based immune systems: exchangeable functional modules. Trends Microbiol. 2011 Nov;19(11):549-56. Epub 2011 Sep 22. Abstract

11. You XY, Liu C, Wang SY, Jiang CY, Shah SA, Prangishvili D, She Q, Liu SJ, Garrett RA. Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles. Extremophiles. 2011 Jul;15(4):487-97. doi: 10.1007/s00792-011-0379-y. Epub 2011 May 24. Full text

10. Snyder JC, Brumfield SK, Peng N, She Q, Young MJ. Sulfolobus Turreted Icosahedral Virus c92 protein responsible for formation of pyramid-like cellular lysis structures. J Virol. 2011 Apr 27. [Epub ahead of print] Abstract

9. Lintner NG, Kerou M, Brumfield SK, Graham S, Liu H, Naismith JH, Sdano M, Peng N, She Q, Copie V, Young MJ, White MF, Lawrence CM. (2011) Structural and functional characterization of an archaeal CASCADE complex for CRISPR-mediated viral defense. J Biol Chem. 2011 Apr 20. [Epub ahead of print] Abstract

8. Scheele U, Erdmann S, Ungewickell EJ, Felisberto-Rodrigues C, Ortiz-Lombardía M, Garrett RA. (2011) Chaperone Role for Proteins p618 and p892 in the Extra-cellular Tail Development of Acidianus Two-tailed Virus ATV. J Virol. 2011 Mar 2. [Epub ahead of print] Abstract

7. Guo, L., Brugger, K., Liu, C., Shah, S. A., Zheng, H., Zhu, Y., Wang, S., Lillestol, R. K., Chen, L., Frank, J., Prangishvili, D., Paulin, L., She, Q., Huang, L. and Garrett, R. A. (2011) Genome Analyses of Icelandic Strains of Sulfolobus islandicus: Model Organisms for Genetic and Virus-Host Interaction Studies. J Bacteriol. (in press) Abstract

6. Peng, N., Ao, X., Liang, Y. X., She, Q. (2011) Archaeal promoter architecture and mechanism of gene activation. Biochem Soc Trans 39: 99-103. Abstract

5. Garrett, R. A., Shah, S. A., Vestergaard, G., Deng, L., Gudbergsdottir, S., Kenchappa, C. S., Erdmann, S., She, Q. (2011) CRISPR-based immune systems of the Sulfolobales: complexity and diversity. Biochem Soc Trans 39: 51-57. Abstract

4. Gudbergsdottir, S., Deng, L., Chen, Z., Jensen, J.V., Jensen, L.R., She, Q.*, Garrett, R.A.* (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: 35-49. Full Content

3. Contursi, P., D'Ambrosio, K., Pirone, L., Pedone, E., Aucelli, T., She, Q., De Simone, G., Bartolucci, S. (2011) c68 from the Sulfolobus islandicus plasmid/virus pSSVx is a novel member of the AbrB-like transcription factor family. Biochem J. (in press) Abstract

2. Zhu, X., Liu, W., Lametsch, R., Aarestrup, F., Shi, C., She, Q.*, Shi, X.*, Knochel, S. (2011) Phenotypic, Proteomic, and Genomic Characterization of a Putative ABC-transporter Permease Involved in Listeria monocytogenes Biofilm Formation. Foodborne Pathog Dis. (in press) Abstract

1. Oke, M., Kerou, M., Liu, H., Peng, X., Garrett, R.A., Prangishvili, D., Naismith, J.H., White, M.F. (2011) A dimeric Rep protein initiates replication of a linear archaeal virus genome: implications for the Rep mechanism and viral replication. J Virol 85: 925-931. Abstract

2010

6. Contursi, P., Cannio, R., She, Q. (2010) Transcription termination in the plasmid/virus hybrid pSSVx from Sulfolobus islandicus. Extremophiles 14: 453-463.

5. Zhang, C., Guo, L., Deng, L., Wu, Y., Liang, Y., Huang, L., She, Q. (2010) Revealing the essentiality of multiple archaeal pcna genes using a mutant propagation assay based on an improved knockout method. Microbiology 156: 3386-3397.

4. Garrett, R.A., Prangishvili, D., Shah, S.A., Reuter, M., Stetter, K.O., Peng, X. (2010) Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles. Environ Microbiol 12: 2918-2930.

3. Goulet, A,, Vestergaard, G., Felisberto-Rodrigues, C., Campanacci, V., Garrett, R.A., Cambillau, C., Ortiz-Lombardia, M. (2010) Getting the best out of long-wavelength X-rays: de novo chlorine/sulfur SAD phasing of a structural protein from ATV. Acta Crystallogr D Biol Crystallogr 66: 304-308.

2. Oke, M., Carter, L.G., Johnson, K,A,, Liu, H., McMahon, S.A., Yan, X., Kerou, M., Weikart, N.D., Kadi, N., Sheikh, M.A., Schmelz, S., Dorward, M., Zawadzki, M., Cozens, C., Falconer, H., Powers, H., Overton, I.M., van Niekerk, C.A., Peng, X., Patel, P., Garrett, R.A., Prangishvili, D., Botting, C.H., Coote, P.J., Dryden, D.T., Barton, G.J., Schwarz-Linek, U., Challis, G.L., Taylor, G.L., White, M.F., Naismith, J.H. (2010) The Scottish Structural Proteomics Facility: targets, methods and outputs. J Struct Funct Genomics 11: 167-180.

1. Shah, S.A., Garrett, R.A. (2010) CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems. Res Microbiol

2009

8. Peng, N., Xia, Q., Chen, Z., Liang, Y.X., She, Q. (2009) An upstream activation element exerting differential transcriptional activation on an archaeal promoter. Mol Microbiol 74: 928-939.

7. Deng, L., Zhu, H., Chen, Z., Liang, Y.X., She, Q. (2009) Unmarked gene deletion and host-vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Extremophiles 13: 735-746.

6. She, Q., Zhang, C., Deng, L., Peng, N., Chen, Z., Liang, Y.X. (2009) Genetic analyses in the hyperthermophilic archaeon Sulfolobus islandicus. Biochem Soc Trans 37: 92-96.

5. Shah, S.A., Hansen, N.R., Garrett, R.A. (2009) Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism. Biochem Soc Trans 37: 23-28.

4. Redder, P., Peng, X., Brugger, K., Shah, S.A., Roesch, F., Greve, B., She, Q., Schleper, C., Forterre, P., Garrett, R.A., Prangishvili, D. (2009) Four newly isolated fuselloviruses from extreme geothermal environments reveal unusual morphologies and a possible interviral recombination mechanism. Environ Microbiol 11: 2849-2862.

3. Pichon, S., Bouchon, D., Cordaux, R., Chen, L., Garrett, R.A., Greve, P. (2009) Conservation of the Type IV secretion system throughout Wolbachia evolution. Biochem Biophys Res Commun 385: 557-562.

2. Lillestol, R.K., Shah, S.A., Brugger, K., Redder, P., Phan, H., Christiansen, J., Garrett, R.A. (2009) CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol Microbiol 72: 259-272.

1. Basta T, Smyth J, Forterre P, Prangishvili D, Peng X. (2009) Novel archaeal plasmid pAH1 and its interactions with the lipothrixvirus AFV1. Mol Microbiol 72: 23-34.

2008

9. Peng, X. (2008) Evidence for the horizontal transfer of an integrase gene from a fusellovirus to a pRN-like plasmid within a single strain of Sulfolobus and the implications for plasmid survival. Microbiology 154: 383-91.

7. Vestergaard, G., Aramayo, R., Basta, T., Häring, M., Peng, X., Brügger, K., Chen, L., Rachel, R., Boisset, N., Garrett, R.A. & Prangishvili, D. Structure of the Acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses from the hyperthermophilic genus Acidianus. J. Virol., 82, 371-381, 2008.

6. Bize, A., Peng, X., Prokofeva, M., MacLellan, K., Lucas, S., Forterre, P., Garrett, R.A., Bonch-Osmolovskaya, A. & Prangishvili, D. Viruses in acidic environments of the Kamchatka Peninsula. Res. Microbiol. 159, 358-366, 2008.

5. Prangishvili, P., Basta, T. & Garrett, R.A. Diversity of crenarchaeal viruses: morphotypes and genomes. Encyclopedia Virology 3rd Edition, Elsevier Ltd., in press.

4. Basta, T., Garrett, R.A., Prangishvili, D. Viruses of the Archaea. Encyclopedia Life Sciences, J. Wiley Ltd., in press.

3. Vestergaard, G., Shah, S.A., Bize, A., Reitberger, W., Reuter, M., Phan, H., Briegel, A., Rachel, R., Garrett, R.A. & Prangishvili, D. SRV, a new rudiviral isolate from Stygioglobus and the interplay of crenarchaeal rudiviruses with the host viral-defence CRISPR system. J. Bacteriol., 190, 6837-6845, 2008.

2. Zhu, X., Long, F., Chen, Y., Knochel, S., She, Q.*, Shi, X.* (2008) A putative ABC transporter is involved in negative regulation of biofilm formation by Listeria monocytogenes. Appl Environ Microbiol 74: 7675-7683.

1. Norman, A., Hansen, L.H., She, Q., Sorensen, S,J. (2008) Nucleotide sequence of pOLA52: a conjugative IncX1 plasmid from Escherichia coli which enables biofilm formation and multidrug efflux. Plasmid 60: 59-74.

1999-2007

Arnold, H.P., She, Q., Phan, H., Stedman, K., Prangishvili, D., Holz, I., Kristjansson, J.K., Garrett, R.A. & Zillig, W. The genetic element pSSVx of the extremely thermophilkic crenarchaeon Sulfolobus is a hybrid between a plasmid and a virus. Molec. Microbiol. 34, 217-226, 1999.

Tolstrup, N., Sensen, C.W., Garrett, R.A. & Clausen, I.G. Two different and highly organized mechanisms of translation intitiation in the archaeon Sulfolobus solfataricus. Extremophiles, 4, 175-179, 2000.

She, Q., Confalonieri, F., Zivanovic, Y., Medina, N., Billault, A., Awayez, M.J., Phan Thi-Ngoc, H., Thi Pham, Boi-Tien, van der Oost, J., Duguet, M. & Garrett, R.A. A Bac library and paired PCR approach to mapping and completing the genome sequence of Sulfolobus solfataricus P2. DNA Sequence, 11, 183-192, 2000.

Stedman, K.M., She, Q., Phan, H., Holz, I., Singh, H., Prangishvili, D., Garrett, R.A. & Zillig, W. The pING family of conjugative plasmids from the extremely thermophilic archaeon Sulfolobus islandicus: Insights into recombination and conjugation in Crenarchaeota. J. Bacteriol. 182, 7014-7020, 2000.

Peng, X., Holz, I., Zillig, W., Garrett, R.A. & She, Q. Evolution of the family of pRN plasmids and their integrase-mediated insertion into the chromosome of the Crenarchaeon Sulfolobus solfataricus. J. Mol. Biol. 303, 449-454, 2000.

Redder, P., Faguy, D., Brügger, K., She, Q. & Garrett, R.A. Archaeal Mobile DNA. In “Mobile DNA” (Craig, N. ed.). A.S.M. Press, Washington, D. C. 2002.

She, Q., Peng, X., Zillig, W. & Garrett, R.A. Gene capture events in archaeal chromosomes. Nature, 409, 478, 2001.

Redder, P., She, Q. & Garrett, R.A. Non-autonomous mobile elements in the Crenarchaeon Sulfolobus solfataricus. J. Molec. Biol. 306, 1-6, 2001.

She, Q., Singh, R.K., Confalonieri, F., Zivanovic, Y., Gordon, P., Allard, G., Awayez, M.J., Chan-Weiher, C-Y., Clausen, I.G., Curtis, B., De Moors, A., Erauso, G., Fletcher, C., Gordon, P.M.K., Heikamp de Jong, I., Jeffries, A., Kozera, C.J., Medina, N., Peng, X., Phan Thi-Ngoc, H., Redder, P., Schenk, M.E., Theriault, C., Tolstrup, N., Charlebois, R. L. M., Doolittle, W. F., Duguet, M., Gaasterland, T., Garrett, R.A., Ragan, M., Sensen, C.W. & Van der Oost, J. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. USA, 98, 7835-7840, 2001.

Peng, X., Blum, H., She, Q., Domdey, H., Mallok, S., Brügger, K., Garrett, R.A., Zillig, W. & Prangishvili, D. (2001). Sequences and replication of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus SIFV and some eukaryal viruses. Virology, 291, 226-234, 2001.

Brügger, K., Redder, P., She, Q., Confalonieri, F., Zivanovic, Y. & Garrett, R.A. Mobile elements in archaeal genomes. FEMS Microbiol. Letts. 206, 131-141, 2002.

Redder, P., Faguy, D., Brügger, K., She, Q. & Garrett, R.A. Archaeal Mobile DNA. In “Mobile DNA” (Craig, N.L., Craigie, R., Gellert, M. & Lambovitz, A.M. eds.). A.S.M. Press, Washington, D. C. pp. 1060-1073, 2002.

Stedman, K. M., She, Q., Phan, H., Arnold, H. P., Holz, I., Garrett, R.A. & Zillig, W. Biological and genetic relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2. Res. Microbiol. 154, 295-302, 2003.

Peng, X., Brügger, K., Shen, B., Chen, L., She, Q. & Garrett, R.A. Genus-specific protein binding to the large clusters of DNA repeats (Short Regularly Spaced Repeats) present in Sulfolobus genomes. J. Bacteriol. 185, 2410-2417, 2003.

Bettstetter, M., Peng, X., Garrett, R.A. & Prangishvili, D. AFV1, a novel virus infecting hyperthermophilic archaea of the genus Acidianus. Virology, 315, 68-79, 2003.

Brügger, K., Redder, P. & Skovgaard, M. MUTAGEN: a multiuser tool for annotating genomes. Bioinformatics 19, 2480-2481, 2003.

Prangishvili, D. & Garrett, R.A. Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses. Biochem. Soc. Trans. 32, 204-208, 2004.

Brügger, K., Torarinsson, E., Chen, L. & Garrett, R.A. Shuffling of Sulfolobus genomes by autonomous and non-autonomous mobile elements. Biochem. Soc. Trans. 32, 179-183, 2004.

Garrett, R.A., Redder, P., Greve, B., Brügger, K., Chen, L. & She, Q. Archaeal plasmids. In Plasmid Biology (eds. Funnell, B.E. and Phillips, G. J.) pp. 377-392, ASM Press, Wash. DC, 2004.

Häring, M., Peng, X., Brügger, K., Rachel, R., Stetter, K.O., Garrett, R.A. & Prangishvili, D. Morphology and genome organisation of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae. Virology, 323, 233-242, 2004.

Lundgren, M., Andersson, A., Chen, L., Nilsson, P. & Bernander, R. Three replication origins in Sulfolobus species: Synchronous initation of chromosome replcation and asynchronous tewrmination. Proc. Natl. Acad. Sci. USA, 101, 7046-7051, 2004.

Torarinsson, E., Klenk, H.-P. & Garrett, R.A. Divergent transcriptional and translational signals in Archaea. Environ. Microbiol.7, 47-54, 2005.

Peng, X., Kessler, A., Phan, H., Garrett, R.A. & Prangishvili, D. Multiple variants of the archaeal DNA rudivirus SIRV1 in a single host and a novel mechanism of genome variation. Molec. Microbiol. 54, 366-375, 2004.

Greve, B., Jensen, S., Brügger, K., Zillig, W. & Garrett, R.A.. Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea, 1, 231-239, 2004.

Greve, B, Jensen, S., Phan, H., Brügger, K., Zillig, W., She, Q. & Garrett, R.A. Novel plasmids pTAU4, pORA1 and pTIK4 from Sulfolobus neozealandicus. Archaea, 1, 319-325, 2005.

Tang, T-H., Polacek, N., Zywicki, M., Huber, H., Brügger, K., Garrett, R.A., Bachellerie, J.P. & Hüttenhofer, A. Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Molec. Microbiol. 55, 469-481, 2005.

Häring, M., Vestergaard, G., Rachel, R., Chen, L., Garrett, R.A. & Prangishvili, D. Independent virus development outside a host. Nature, 436, 1101-1102, 2005.

Häring, M., Vestergaard, G., Brügger, K., Rachel, R., Garrett, R.A. & Prangishvili, D. Structure and genome organisation of AFV2, a novel filamentous archaeal virus with unusual terminal structures. J. Bacteriol. 187, 3855-3858, 2005.

Vestergaard, G., Häring, M., Peng, X., Rachel, R., Garrett, R.A. & Prangishvili, D. ARV1, a novel rudivirus infecting the hyperthermophilic genus Acidianus. Virology, 336, 83-92, 2005.

Häring, M., Rachel, R., Peng, X., Garrett, R.A. & Prangishvili, D. Diverse viruses in hot springs of Pozzuoli, Italy, including a unique bottle-shaped virus ABV from a new family the Ampullaviridae. J. Virol. 79, 9904-9911, 2005.

Chen, L., Brügger, K., Skovgaard, M., Redder, P., She, Q.,Torarinsson, E., Greve, B., Awayez, M., Zibat, A., Klenk, H.-P. & Garrett, R.A. The Genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota J. Bacteriol. 187, 4992-4999, 2005.

Prangishvili, D. & Garrett, R.A. Viruses of hyperthermophilic crenarchaea. Trends Microbiology. 13, 535-542, 2005.

Peng, X., Garrett, R.A., Häring, M. & Prangishvili, D. (2005) "Thermostable DNA polymerase of the archaeal ampullavirus ABV and its applications". European Patent Office number is 06290764.7.

Prangishvili, D., Garrett, R.A. & Koonin, E. Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Research. 117, 52-67, 2006.

Redder, P. & Garrett, R.A. Mutations and rearrangements in the genome of Sulfolobus solfataricus P2. J. Bacteriol. 188, 4198-4206, 2006.

Prangishvili, D., Vestergaard, G., Häring, M., Aramayo, R., Basta, T., Rachel, R. & Garrett, R.A. Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle. J. Molec. Biol. 359, 1203-1216, 2006.

Lillestøl, R., Redder, P., Garrett, R.A. & Brügger, K. A putative viral defence mechanism in archaeal cells. Archaea, 2, 59-72, 2006.

Prangishvili, D., Forterre, P. & Garrett, R.A. Viruses of the Archaea: a unifying view. Nature Rev. Microbiology, 4, 837-848, 2006.

Goulet, A., Spinelli, S., Campanacci, V., Porciero, S., Blangy, S., Garrett, R.A., van Tilbeurgh, H., Leuillot, N., Basta, T., Prangishvili, D. & Cambillau, C. Crystallization and preliminary X-ray diffraction analysis of protein 14 from Sulfolobus islandicus filamentous virus (SIFV). Acta Cryst. F62, 884-886, 2006

Brügger, K. The Sulfolobus Database. Nucleic Acids Res. D413-415, 2007

Garrett, R.A. & Klenk, H.P. (Eds.) Archaea: Evolution, Physiology and Molecular Biology. Blackwell Publishing, Oxford, 2007.

Brügger, K., Peng, X. & Garrett, R.A. Sulfolobus genomes: mechanisms of rearrangement and change. In: Archaea: Evolution, Physiology and Molecular Biology, (Garrett, R.A. & Klenk, H.P. Eds.). Blackwell Publishing, Oxford, pp. 95-104, 2007.

Brügger, K., Chen, L., Stark, M., Zibat, A, Redder, P., Ruepp, A., Awayez, M, She, Q., Garrett, R.A. & Klenk, H-P. The genome of Hyperthermus butylicus: a sulphur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108oC. Archaea, 2, 127-135, 2007.

Peng, X., Basta, T., Häring, M., Garrett, R.A. & Prangishvili, D. Genome of the Acidianus bottle-shaped virus and insights into the replication and packaging mechanisms. Virology, 364, 237-243, 2007.