My NCBISign In
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
Kira S Makarova, Nick V Grishin, Svetlana A Shabalina, Yuri I Wolf, Eugene V Koonin
Biol Direct. 2006; 1: 7. Published online 2006 March 16. doi: 10.1186/1745-6150-1-7
PMCID:
PMC1462988
Abstract Full Text PDF–884K Supplementary Material

Is Cited by the Following 112 Articles in this Archive:

Characterization of the CRISPR/Cas Subtype I-A System of the Hyperthermophilic Crenarchaeon Thermoproteus tenax
André Plagens, Britta Tjaden, Anna Hagemann, Lennart Randau, Reinhard Hensel
J Bacteriol. 2012 May; 194(10): 2491–2500. doi: 10.1128/JB.00206-12
PMCID:
PMC3347209
Free in PMC on 2012/11/01
Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs
Benjamin Bolduc, Daniel P. Shaughnessy, Yuri I. Wolf, Eugene V. Koonin, Francisco F. Roberto, Mark Young
J Virol. 2012 May; 86(10): 5562–5573. doi: 10.1128/JVI.07196-11
PMCID:
PMC3347303
Free in PMC on 2012/11/01
Persisting Viral Sequences Shape Microbial CRISPR-based Immunity
Ariel D. Weinberger, Christine L. Sun, Mateusz M. Pluciński, Vincent J. Denef, Brian C. Thomas, Philippe Horvath, Rodolphe Barrangou, Michael S. Gilmore, Wayne M. Getz, Jillian F. Banfield
PLoS Comput Biol. 2012 April; 8(4): e1002475. Published online 2012 April 19. doi: 10.1371/journal.pcbi.1002475
PMCID:
PMC3330103
Abstract Full Text PDF–5.3M Supplementary Material
Identification and Characterization of Small RNAs in the Hyperthermophilic Archaeon Sulfolobus solfataricus
Ning Xu, Yan Li, Ying-Tao Zhao, Li Guo, Yuan-Yuan Fang, Jian-Hua Zhao, Xiu-Jie Wang, Li Huang, Hui-Shan Guo
PLoS One. 2012; 7(4): e35306. Published online 2012 April 13. doi: 10.1371/journal.pone.0035306
PMCID:
PMC3325985
Abstract Full Text PDF–641K Supplementary Material
Reconstructing Viral Genomes from the Environment Using Fosmid Clones: The Case of Haloviruses
Inmaculada Garcia-Heredia, Ana-Belen Martin-Cuadrado, Francisco J. M. Mojica, Fernando Santos, Alex Mira, Josefa Antón, Francisco Rodriguez-Valera
PLoS One. 2012; 7(3): e33802. Published online 2012 March 30. doi: 10.1371/journal.pone.0033802
PMCID:
PMC3316494
Abstract Full Text PDF–2.1M Supplementary Material
Crystal Structure of Streptococcus pyogenes Csn2 Reveals Calcium-Dependent Conformational Changes in Its Tertiary and Quaternary Structure
Yoon Koo, Du-kyo Jung, Euiyoung Bae
PLoS One. 2012; 7(3): e33401. Published online 2012 March 30. doi: 10.1371/journal.pone.0033401
PMCID:
PMC3316568
Abstract Full Text PDF–1.5M Supplementary Material
Nature and Intensity of Selection Pressure on CRISPR-Associated Genes
Nobuto Takeuchi, Yuri I. Wolf, Kira S. Makarova, Eugene V. Koonin
J Bacteriol. 2012 March; 194(5): 1216–1225. doi: 10.1128/JB.06521-11
PMCID:
PMC3294813
Abstract Full Text PDF–730K
Insights into Chi recognition from the structure of an AddAB-type helicase–nuclease complex
Kayarat Saikrishnan, Joseph T Yeeles, Neville S Gilhooly, Wojciech W Krajewski, Mark S Dillingham, Dale B Wigley
EMBO J. 2012 March 21; 31(6): 1568–1578. Published online 2012 February 3. doi: 10.1038/emboj.2012.9
PMCID:
PMC3321194
Abstract Full Text PDF–1.4M Supplementary Material
Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity
Ae-Ran Kwon, Ji-Hun Kim, Sung Jean Park, Ki-Young Lee, Yu-Hong Min, Hookang Im, Ingyun Lee, Kyu-Yeon Lee, Bong-Jin Lee
Nucleic Acids Res. 2012 May; 40(9): 4216–4228. Published online 2012 January 11. doi: 10.1093/nar/gkr1305
PMCID:
PMC3351183
Abstract Full Text PDF–4.9M Supplementary Material
Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs
Caryn R. Hale, Sonali Majumdar, Joshua Elmore, Neil Pfister, Mark Compton, Sara Olson, Alissa M. Resch, Claiborne V. C. Glover, III, Brenton R. Graveley, Rebecca M. Terns, Michael P. Terns
Mol Cell. Author manuscript; available in PMC 2013 February 10.
Published in final edited form as: Mol Cell. 2012 February 10; 45(3): 292–302. Published online 2012 January 5. doi: 10.1016/j.molcel.2011.10.023
PMCID:
PMC3278580
Free in PMC on 2013/02/10
High-temperature protein G is essential for activity of the Escherichia coli clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system
Ido Yosef, Moran G. Goren, Ruth Kiro, Rotem Edgar, Udi Qimron
Proc Natl Acad Sci U S A. 2011 December 13; 108(50): 20136–20141. Published online 2011 November 23. doi: 10.1073/pnas.1113519108
PMCID:
PMC3250196
Free in PMC on 2012/06/13
Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems
Kira S. Makarova, Yuri I. Wolf, Sagi Snir, Eugene V. Koonin
J Bacteriol. 2011 November; 193(21): 6039–6056. doi: 10.1128/JB.05535-11
PMCID:
PMC3194920
Abstract Full Text PDF–3.3M Supplementary Material
Complete Genome Sequence of Bifidobacterium animalis subsp. lactis BLC1
Francesca Bottacini, Fabio Dal Bello, Francesca Turroni, Christian Milani, Sabrina Duranti, Elena Foroni, Alice Viappiani, Francesco Strati, Diego Mora, Douwe van Sinderen, Marco Ventura
J Bacteriol. 2011 November; 193(22): 6387–6388. doi: 10.1128/JB.06079-11
PMCID:
PMC3209193
Abstract Full Text PDF–36K
Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference
Natalia Beloglazova, Pierre Petit, Robert Flick, Greg Brown, Alexei Savchenko, Alexander F Yakunin
EMBO J. 2011 November 16; 30(22): 4616–4627. Published online 2011 October 18. doi: 10.1038/emboj.2011.377
PMCID:
PMC3243599
Free in PMC on 2012/11/16
The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota
Bettina Siebers, Melanie Zaparty, Guenter Raddatz, Britta Tjaden, Sonja-Verena Albers, Steve D. Bell, Fabian Blombach, Arnulf Kletzin, Nikos Kyrpides, Christa Lanz, André Plagens, Markus Rampp, Andrea Rosinus, Mathias von Jan, Kira S. Makarova, Hans-Peter Klenk, Stephan C. Schuster, Reinhard Hensel
PLoS One. 2011; 6(10): e24222. Published online 2011 October 7. doi: 10.1371/journal.pone.0024222
PMCID:
PMC3189178
Abstract Full Text PDF–469K Supplementary Material
Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs
Rudi F Vogel, Melanie Pavlovic, Matthias A Ehrmann, Arnim Wiezer, Heiko Liesegang, Stefanie Offschanka, Sonja Voget, Angel Angelov, Georg Böcker, Wolfgang Liebl
Microb Cell Fact. 2011; 10(Suppl 1): S6. Published online 2011 August 30. doi: 10.1186/1475-2859-10-S1-S6
PMCID:
PMC3231932
Abstract Full Text PDF–828K Supplementary Material
The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli
Rimantas Sapranauskas, Giedrius Gasiunas, Christophe Fremaux, Rodolphe Barrangou, Philippe Horvath, Virginijus Siksnys
Nucleic Acids Res. 2011 November; 39(21): 9275–9282. Published online 2011 August 3. doi: 10.1093/nar/gkr606
PMCID:
PMC3241640
Abstract Full Text PDF–1.7M Supplementary Material
Structural and Biochemical Analysis of Nuclease Domain of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Protein 3 (Cas3)
Sabin Mulepati, Scott Bailey
J Biol Chem. 2011 September 9; 286(36): 31896–31903. Published online 2011 July 20. doi: 10.1074/jbc.M111.270017
PMCID:
PMC3173111
Free in PMC on 2012/09/09
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems
Kira S Makarova, L Aravind, Yuri I Wolf, Eugene V Koonin
Biol Direct. 2011; 6: 38. Published online 2011 July 14. doi: 10.1186/1745-6150-6-38
PMCID:
PMC3150331
Abstract Full Text PDF–2.9M Supplementary Material
Non-Identity-Mediated CRISPR-Bacteriophage Interaction Mediated via the Csy and Cas3 Proteins
Kyle C. Cady, George A. O'Toole
J Bacteriol. 2011 July; 193(14): 3433–3445. doi: 10.1128/JB.01411-10
PMCID:
PMC3133329
Abstract Full Text PDF–1.3M Supplementary Material
Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca2+-dependent Double-stranded DNA Binding Activity
Ki Hyun Nam, Igor Kurinov, Ailong Ke
J Biol Chem. 2011 September 2; 286(35): 30759–30768. Published online 2011 June 21. doi: 10.1074/jbc.M111.256263
PMCID:
PMC3162437
Free in PMC on 2012/09/02
Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi
Kounthéa Phok, Annick Moisan, Dana Rinaldi, Nicolas Brucato, Agamemnon J Carpousis, Christine Gaspin, Béatrice Clouet-d'Orval
BMC Genomics. 2011; 12: 312. Published online 2011 June 13. doi: 10.1186/1471-2164-12-312
PMCID:
PMC3124441
Abstract Full Text PDF–1.4M Supplementary Material
Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence
Ekaterina Semenova, Matthijs M. Jore, Kirill A. Datsenko, Anna Semenova, Edze R. Westra, Barry Wanner, John van der Oost, Stan J. J. Brouns, Konstantin Severinov
Proc Natl Acad Sci U S A. 2011 June 21; 108(25): 10098–10103. Published online 2011 June 6. doi: 10.1073/pnas.1104144108
PMCID:
PMC3121866
Abstract Full Text PDF–1.1M Supplementary Material
Diversity, Evolution, and Functionality of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Regions in the Fire Blight Pathogen Erwinia amylovora
Fabio Rezzonico, Theo H. M. Smits, Brion Duffy
Appl Environ Microbiol. 2011 June; 77(11): 3819–3829. doi: 10.1128/AEM.00177-11
PMCID:
PMC3127596
Abstract Full Text PDF–1.9M Supplementary Material
CRISPR Inhibition of Prophage Acquisition in Streptococcus pyogenes
Takashi Nozawa, Nayuta Furukawa, Chihiro Aikawa, Takayasu Watanabe, Bijaya Haobam, Ken Kurokawa, Fumito Maruyama, Ichiro Nakagawa
PLoS One. 2011; 6(5): e19543. Published online 2011 May 6. doi: 10.1371/journal.pone.0019543
PMCID:
PMC3089615
Abstract Full Text PDF–447K Supplementary Material
RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions
Blake Wiedenheft, Esther van Duijn, Jelle B. Bultema, Sakharam P. Waghmare, Kaihong Zhou, Arjan Barendregt, Wiebke Westphal, Albert J. R. Heck, Egbert J. Boekema, Mark J. Dickman, Jennifer A. Doudna
Proc Natl Acad Sci U S A. 2011 June 21; 108(25): 10092-10097. Published online 2011 May 2. doi: 10.1073/pnas.1102716108
Correction in:
Proc Natl Acad Sci U S A. 2011 September 6; 108(36): 15010.
PMCID:
PMC3121849
Abstract Full Text PDF–1.0M Supplementary Material Correction
The CRISPR/Cas Immune System Is an Operon Regulated by LeuO, H-NS, and Leucine-Responsive Regulatory Protein in Salmonella enterica Serovar Typhi
L. Medina-Aparicio, J. E. Rebollar-Flores, A. L. Gallego-Hernández, A. Vázquez, L. Olvera, R. M. Gutiérrez-Ríos, E. Calva, I. Hernández-Lucas
J Bacteriol. 2011 May; 193(10): 2396–2407. doi: 10.1128/JB.01480-10
PMCID:
PMC3133143
Abstract Full Text PDF–1.5M Supplementary Material
CRISPR-Based Adaptive Immune Systems
Michael P. Terns, Rebecca M. Terns
Curr Opin Microbiol. Author manuscript; available in PMC 2012 June 1.
Published in final edited form as: Curr Opin Microbiol. 2011 June; 14(3): 321–327. Published online 2011 April 29. doi: 10.1016/j.mib.2011.03.005
PMCID:
PMC3119747
Free in PMC on 2012/06/01
The use of microbead-based spoligotyping for Mycobacterium tuberculosis complex to evaluate the quality of the conventional method: Providing guidelines for Quality Assurance when working on membranes
Edgar Abadia, Jian Zhang, Viviana Ritacco, Kristin Kremer, Raymond Ruimy, Leen Rigouts, Harrison Magdinier Gomes, Atiná Ribeiro Elias, Maryse Fauville-Dufaux, Karolien Stoffels, Voahangy Rasolofo-Razanamparany, Darío Garcia de Viedma, Marta Herranz, Sahal Al-Hajoj, Nalin Rastogi, Carlo Garzelli, Enrico Tortoli, Philip N Suffys, Dick van Soolingen, Guislaine Refrégier, Christophe Sola
BMC Infect Dis. 2011; 11: 110. Published online 2011 April 28. doi: 10.1186/1471-2334-11-110
PMCID:
PMC3107175
Abstract Full Text PDF–366K Supplementary Material
Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)
Nathanael G. Lintner, Melina Kerou, Susan K. Brumfield, Shirley Graham, Huanting Liu, James H. Naismith, Matthew Sdano, Nan Peng, Qunxin She, Valérie Copié, Mark J. Young, Malcolm F. White, C. Martin Lawrence
J Biol Chem. 2011 June 17; 286(24): 21643–21656. Published online 2011 April 20. doi: 10.1074/jbc.M111.238485
PMCID:
PMC3122221
Free in PMC on 2012/06/17
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