DNA-guided DNA interference by a prokaryotic Argonaute

Nature

Volumn 507, Issue 7491, 2014, Pages 258-261

  Swarts, Daan C ^a   Jore, Matthijs M ^a   Westra, Edze R ^a   Zhu, Yifan ^a   Janssen, Jorijn H ^a   Snijders, Ambrosius P ^b   Wang, Yanli ^c   Patel, Dinshaw J ^d   Berenguer, José ^e   Brouns, Stan J J ^a   Van Der Oost, John ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^c INSTITUTE OF BIOPHYSICS   (China)

^d MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^e CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARGONAUTE PROTEIN; COMPLEMENTARY DNA; DEOXYCYTIDINE; DNA; NUCLEOTIDE;

BIOINFORMATICS; DNA; EUKARYOTE; MOLECULAR ANALYSIS; PROKARYOTE;

ARTICLE; BACTERIUM; DNA CLEAVAGE; DNA GUIDED DNA INTERFERENCE; DNA STRAND; GENETIC REGULATION; HOST RESISTANCE; NONHUMAN; PLASMID; PRIORITY JOURNAL; STRUCTURAL HOMOLOGY; THERMUS THERMOPHILUS;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA; THERMUS THERMOPHILUS;

ARGONAUTE PROTEINS; BASE PAIRING; BASE SEQUENCE; DEOXYCYTIDINE; DNA; DNA CLEAVAGE; GENE SILENCING; PHOSPHORYLATION; PLASMIDS; PROKARYOTIC CELLS; THERMUS THERMOPHILUS;

EID: 84896316351     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature12971     Document Type: Article

References (31)

1. Ketting, R. F. microRNA biogenesis and function: an overview. Adv. Exp. Med. Biol. 700, 1-14 (2011).
2. Joshua-Tor, L. & Hannon, G. J. Ancestral roles of small RNAs: an Ago-centric perspective. Cold Spring Harb. Perspect. Biol. 3, a003772 (2011).
3. Makarova, K. S., Wolf, Y. I., van der Oost, J. & Koonin, E. V. 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, 29 (2009).
4. Koyama, Y.,Hoshino, T., Tomizuka, N.&Furukawa, K.Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp. J. Bacteriol. 166, 338-340 (1986).
5. Averhoff, B. Shuffling genes around in hot environments: the unique DNA transporter of Thermus thermophilus. FEMS Microbiol. Rev. 33, 611-626 (2009).
6. Gregory, S. T. & Dahlberg, A. E. Transposition of an insertion sequence, ISTth7, in the genome of the extreme thermophile Thermus thermophilus HB8. FEMS Microbiol. Lett. 289, 187-192 (2008).
7. Liu, J. et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305, 1437-1441 (2004).
8. Wang, Y., Sheng, G., Juranek, S., Tuschl, T. & Patel, D. J. Structure of the guide-strand-containing argonaute silencing complex.Nature 456,209-213(2008).
9. Yuan, Y. R. et al. Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol. Cell 19, 405-419 (2005).
10. Ma, J. B. et al. Structural basis for 59-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434, 666-670 (2005).
11. Nakanishi, K., Weinberg, D. E., Bartel, D. P. & Patel, D. J. Structure of yeast Argonaute with guide RNA. Nature 486, 368-374 (2012).
12. Wang, Y. et al. Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456, 921-926 (2008).
13. Wang, Y. et al. Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461, 754-761 (2009).
14. Frank, F., Sonenberg, N.&Nagar, B. Structural basis for59-nucleotide base-specific recognition of guide RNA by human AGO2. Nature 465, 818-822 (2010).
15. Frank, F.,Hauver, J., Sonenberg, N.&Nagar, B.Arabidopsis ArgonauteMIDdomains use their nucleotide specificity loop to sort small RNAs. EMBO J. 31, 3588-3595 (2012).
16. Collin, R. G., Morgan, H. W., Musgrave, D. R. & Daniel, R. M. Distribution of reverse gyrase in representative species of eubacteria and archaebacteria. FEMSMicrobiol. Lett. 55, 235-240 (1988).
17. Charbonnier, F. & Forterre, P. Comparison of plasmid DNA topology among mesophilic and thermophilic eubacteria and archaebacteria. J. Bacteriol. 176, 1251-1259 (1994).
18. Duguet, M. The helical repeat of DNA at high temperature. Nucleic Acids Res. 21, 463-468 (1993).
19. Westra, E. R. et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invaderDNAby Cascade and Cas3. Mol. Cell 46, 595-605 (2012).
20. Bates, A. D. & Maxwell, A. DNA Topology 2nd edn (Oxford Univ. Press, 2005).
21. Elbashir, S. M.,Martinez, J., Patkaniowska, A., Lendeckel, W.& Tuschl, T. Functional anatomyof siRNAs formediating efficientRNAi in Drosophilamelanogasterembryo lysate. EMBO J. 20, 6877-6888 (2001).
22. Sheng, G. et al. Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc. Natl Acad. Sci. USA 111, 652-657 (2013).
23. Olovnikov, I., Chan, K., Sachidanandam, R., Newman, D. K. & Aravin, A. A. Bacterial Argonaute samples the transcriptome to identify foreign DNA. Mol. Cell 51, 594-605 (2013).
24. Travers, A. & Muskhelishvili, G. DNA supercoiling - a global transcriptional regulator for enterobacterial growth? Nature Rev. Microbiol. 3, 157-169 (2005).
25. Rocha, E. P. C.& Danchin, A. Base composition bias might result fromcompetition for metabolic resources. Trends Genet. 18, 291-294 (2002).
26. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
27. Laptenko, O. et al.pH-dependent conformational switch activates the inhibitor of transcription elongation. EMBO J. 25, 2131-2141 (2006).
28. Milne, I. et al. Using Tablet for visual exploration of second-generation sequencing data. Brief. Bioinform. 14, 193-202 (2013).
29. Uliczka, F. et al.Monitoring of gene expression in bacteria during infections using an adaptable set of bioluminescent, fluorescent and colorigenic fusion vectors. PLoS ONE 6, e20425 (2011).
30. Cava, F. et al. Expression and use of superfolder green fluorescent protein at high temperatures in vivo: a tool to study extreme thermophile biology. Environ. Microbiol. 10, 605-613 (2008).
31. Cava, F. et al. Control of the respiratory metabolism of Thermus thermo philus by the nitrate respiration conjugative element NCE. Mol. Microbiol. 64, 630-646 (2007).