James A. Shapiro Curriculum Vitae Publications Blogs    Presentations & Videos Bacteria Genome Engineering Evolution: A view from the 21st Century (June 2011) Courses Contact Me

CRISPRs

 

(Bolotin, Quinquis et al. 2005; Haft, Selengut et al. 2005; Makarova, Grishin et al. 2006; Barrangou, Fremaux et al. 2007; Andersson and Banfield 2008; Beloglazova, Brown et al. 2008; Brouns, Jore et al. 2008; Carte, Wang et al. 2008; Deveau, Barrangou et al. 2008; Horvath, Romero et al. 2008; Sorek, Kunin et al. 2008; Vestergaard, Shah et al. 2008; Horvath, Coute-Monvoisin et al. 2009; Makarova, Wolf et al. 2009; Narberhaus and Vogel 2009; Rousseau, Gonnet et al. 2009; Shah, Hansen et al. 2009; van der Oost and Brouns 2009; van der Oost, Jore et al. 2009; van der Ploeg 2009; Wiedenheft, Zhou et al. 2009; Garneau, Dupuis et al. 2010; Haurwitz, Jinek et al. 2010; Horvath and Barrangou 2010; Marraffini and Sontheimer 2010; Sorokin, Gelfand et al. 2010; Sorokin, Gelfand et al. 2010; Al-Attar, Westra et al. 2011; Blower, Pei et al. 2011; Deltcheva, Chylinski et al. 2011; Garrett, Shah et al. 2011; Garrett, Vestergaard et al. 2011; Jore, Lundgren et al. 2011; Makarova, Aravind et al. 2011; Makarova, Haft et al. 2011; Makarova, Wolf et al. 2011; Semenova, Jore et al. 2011; Terns and Terns 2011; Wiedenheft, Lander et al. 2011; Djordjevic, Djordjevic et al. 2012; Bikard and Marraffini 2013; Watanabe, Nozawa et al. 2013)

 

REFERENCES

 

Al-Attar, S., E. R. Westra, et al. (2011). "Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes." Biol Chem 392(4): 277-289. http://www.ncbi.nlm.nih.gov/pubmed/21294681.

Andersson, A. F. and J. F. Banfield (2008). "Virus population dynamics and acquired virus resistance in natural microbial communities." Science 320(5879): 1047-1050. http://www.ncbi.nlm.nih.gov/pubmed/18497291.

Barrangou, R., C. Fremaux, et al. (2007). "CRISPR provides acquired resistance against viruses in prokaryotes." Science 315(5819): 1709-1712. http://www.ncbi.nlm.nih.gov/pubmed/17379808.

Beloglazova, N., G. Brown, et al. (2008). "A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats." J Biol Chem 283(29): 20361-20371. http://www.ncbi.nlm.nih.gov/pubmed/18482976.

Bikard, D. and L. A. Marraffini (2013). "Control of gene expression by CRISPR-Cas systems." F1000Prime Rep 5: 47. http://www.ncbi.nlm.nih.gov/pubmed/24273648.

Blower, T. R., X. Y. Pei, et al. (2011). "A processed noncoding RNA regulates an altruistic bacterial antiviral system." Nat Struct Mol Biol 18(2): 185-190. http://www.ncbi.nlm.nih.gov/pubmed/21240270.

Bolotin, A., B. Quinquis, et al. (2005). "Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin." Microbiology 151(Pt 8): 2551-2561. http://www.ncbi.nlm.nih.gov/pubmed/16079334.

Brouns, S. J., M. M. Jore, et al. (2008). "Small CRISPR RNAs guide antiviral defense in prokaryotes." Science 321(5891): 960-964. http://www.ncbi.nlm.nih.gov/pubmed/18703739.

Carte, J., R. Wang, et al. (2008). "Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes." Genes Dev 22(24): 3489-3496. http://www.ncbi.nlm.nih.gov/pubmed/19141480.

Deltcheva, E., K. Chylinski, et al. (2011). "CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III." Nature 471(7340): 602-607. http://www.ncbi.nlm.nih.gov/pubmed/21455174.

Deveau, H., R. Barrangou, et al. (2008). "Phage response to CRISPR-encoded resistance in Streptococcus thermophilus." J Bacteriol 190(4): 1390-1400. http://www.ncbi.nlm.nih.gov/pubmed/18065545.

Djordjevic, M., M. Djordjevic, et al. (2012). "CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs." Biol Direct 7(1): 24. http://www.ncbi.nlm.nih.gov/pubmed/22849651.

Garneau, J. E., M.-E. Dupuis, et al. (2010). "The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA." Nature\ 468\(7320\): 67\-71\. .

Garrett, R. A., S. A. Shah, et al. (2011). "CRISPR-based immune systems of the Sulfolobales: complexity and diversity." Biochem Soc Trans 39(1): 51-57. http://www.ncbi.nlm.nih.gov/pubmed/21265746.

Garrett, R. A., G. Vestergaard, et al. (2011). "Archaeal CRISPR-based immune systems: exchangeable functional modules." Trends Microbiol 19(11): 549-556. http://www.ncbi.nlm.nih.gov/pubmed/21945420.

Haft, D. H., J. Selengut, et al. (2005). "A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes." PLoS Comput Biol 1(6): e60. http://www.ncbi.nlm.nih.gov/pubmed/16292354.

Haurwitz, R. E., M. Jinek, et al. (2010). "Sequence- and structure-specific RNA processing by a CRISPR endonuclease." Science 329(5997): 1355-1358. http://www.ncbi.nlm.nih.gov/pubmed/20829488.

Horvath, P. and R. Barrangou (2010). "CRISPR/Cas, the immune system of bacteria and archaea." Science 327(5962): 167-170. http://www.ncbi.nlm.nih.gov/pubmed/20056882.

Horvath, P., A. C. Coute-Monvoisin, et al. (2009). "Comparative analysis of CRISPR loci in lactic acid bacteria genomes." Int J Food Microbiol 131(1): 62-70. http://www.ncbi.nlm.nih.gov/pubmed/18635282.

Horvath, P., D. A. Romero, et al. (2008). "Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus." J Bacteriol 190(4): 1401-1412. http://www.ncbi.nlm.nih.gov/pubmed/18065539.

Jore, M. M., M. Lundgren, et al. (2011). "Structural basis for CRISPR RNA-guided DNA recognition by Cascade." Nat Struct Mol Biol 18(5): 529-536. http://www.ncbi.nlm.nih.gov/pubmed/21460843.

Makarova, K. S., L. Aravind, et al. (2011). "Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems." Biol Direct 6: 38. http://www.ncbi.nlm.nih.gov/pubmed/21756346.

Makarova, K. S., N. V. Grishin, et al. (2006). "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." Biol Direct 1: 7. http://www.ncbi.nlm.nih.gov/pubmed/16545108.

Makarova, K. S., D. H. Haft, et al. (2011). "Evolution and classification of the CRISPR-Cas systems." Nat Rev Microbiol 9(6): 467-477. http://www.ncbi.nlm.nih.gov/pubmed/21552286.

Makarova, K. S., Y. I. Wolf, et al. (2011). "Defense islands in bacterial and archaeal genomes and prediction of novel defense systems." J Bacteriol 193(21): 6039-6056. http://www.ncbi.nlm.nih.gov/pubmed/21908672.

Makarova, K. S., Y. I. Wolf, et al. (2009). "Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements." Biol Direct 4(1): 29. http://www.ncbi.nlm.nih.gov/pubmed/19706170.

Marraffini, L. A. and E. J. Sontheimer (2010). "CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea." Nat Rev Genet 11(3): 181-190. http://www.ncbi.nlm.nih.gov/pubmed/20125085.

Narberhaus, F. and J. Vogel (2009). "Regulatory RNAs in prokaryotes: here, there and everywhere." Mol Microbiol 74(2): 261-269. http://www.ncbi.nlm.nih.gov/pubmed/19732342.

Rousseau, C., M. Gonnet, et al. (2009). "CRISPI: a CRISPR interactive database." Bioinformatics 25(24): 3317-3318. http://www.ncbi.nlm.nih.gov/pubmed/19846435.

Semenova, E., M. M. Jore, et al. (2011). "Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence." Proc Natl Acad Sci U S A 108(25): 10098-10103. http://www.ncbi.nlm.nih.gov/pubmed/21646539.

Shah, S. A., N. R. Hansen, et al. (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. http://www.ncbi.nlm.nih.gov/pubmed/19143596.

Sorek, R., V. Kunin, et al. (2008). "CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea." Nat Rev Microbiol 6(3): 181-186. http://www.ncbi.nlm.nih.gov/pubmed/18157154.

Sorokin, V. A., M. S. Gelfand, et al. (2010). "Evolutionary dynamics of clustered irregularly interspaced short palindromic repeat systems in the ocean metagenome." Appl Environ Microbiol 76(7): 2136-2144. http://www.ncbi.nlm.nih.gov/pubmed/20118362.

Sorokin, V. A., M. S. Gelfand, et al. (2010). "Evolutionary dynamics of CRISPR systems in the Ocean metagenome." Appl Environ Microbiol 76(7): 2136-2144. http://www.ncbi.nlm.nih.gov/pubmed/20118362.

Terns, M. P. and R. M. Terns (2011). "CRISPR-based adaptive immune systems." Curr Opin Microbiol 14(3): 321-327. http://www.ncbi.nlm.nih.gov/pubmed/21531607.

van der Oost, J. and S. J. Brouns (2009). "RNAi: prokaryotes get in on the act." Cell 139(5): 863-865. http://www.ncbi.nlm.nih.gov/pubmed/19945373.

van der Oost, J., M. M. Jore, et al. (2009). "CRISPR-based adaptive and heritable immunity in prokaryotes." Trends Biochem Sci 34(8): 401-407. http://www.ncbi.nlm.nih.gov/pubmed/19646880.

van der Ploeg, J. R. (2009). "Analysis of CRISPR in Streptococcus mutans suggests frequent occurrence of acquired immunity against infection by M102-like bacteriophages." Microbiology 155(Pt 6): 1966-1976. http://www.ncbi.nlm.nih.gov/pubmed/19383692.

Vestergaard, G., S. A. Shah, et al. (2008). "Stygiolobus rod-shaped virus and the interplay of crenarchaeal rudiviruses with the CRISPR antiviral system." J Bacteriol 190(20): 6837-6845. http://www.ncbi.nlm.nih.gov/pubmed/18723627.

Watanabe, T., T. Nozawa, et al. (2013). "CRISPR regulation of intraspecies diversification by limiting IS transposition and intercellular recombination." Genome Biol Evol 5(6): 1099-1114. http://www.ncbi.nlm.nih.gov/pubmed/23661565.

Wiedenheft, B., G. C. Lander, et al. (2011). "Structures of the RNA-guided surveillance complex from a bacterial immune system." Nature 477(7365): 486-489. http://www.ncbi.nlm.nih.gov/pubmed/21938068.

Wiedenheft, B., K. Zhou, et al. (2009). "Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense." Structure 17(6): 904-912. http://www.ncbi.nlm.nih.gov/pubmed/19523907.