Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 52, 2012, Pages 21480-21485

  Morse, Robert P ^a   Nikolakakis, Kiel C ^b   Willett, Julia L E ^b   Gerrick, Elias ^a   Low, David A ^b   Hayes, Christopher S ^b   Goulding, Celia W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

complementation; Bacterial competition; Structural biology; tRNase activity

Indexed keywords

DEOXYRIBONUCLEASE; TOXIN; TRANSFER RNA;

ARTICLE; BURKHOLDERIA PSEUDOMALLEI; CONTACT DEPENDENT GROWTH INHIBITION SYSTEM; CONTROLLED STUDY; CRYSTAL STRUCTURE; ESCHERICHIA COLI; GENE SEQUENCE; GROWTH INHIBITION; IMMUNITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CLEAVAGE; TOXICITY;

BACTERIAL PROTEINS; BACTERIAL TOXINS; BURKHOLDERIA PSEUDOMALLEI; CONTACT INHIBITION; CRYSTALLOGRAPHY, X-RAY; DNA; ENDONUCLEASES; ESCHERICHIA COLI; IMMUNITY; MODELS, MOLECULAR; MULTIGENE FAMILY; PROTEIN STRUCTURE, SECONDARY;

BACTERIA (MICROORGANISMS); BURKHOLDERIA PSEUDOMALLEI; ESCHERICHIA COLI;

EID: 84871824016     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1216238110     Document Type: Article

References (30)

1. Aoki SK, et al. (2010) A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria. Nature 468(7322):439-442.
2. Aoki SK, et al. (2005) Contact-dependent inhibition of growth in Escherichia coli. Science 309(5738):1245-1248. (Pubitemid 41170918)
3. Kajava AV, et al. (2001) Beta-helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins. Mol Microbiol 42(2):279-292. (Pubitemid 32990120)
4. Aoki SK, et al. (2008) Contact-dependent growth inhibition requires the essential outer membrane protein BamA (YaeT) as the receptor and the inner membrane transport protein AcrB. Mol Microbiol 70(2):323-340.
5. Nikolakakis K, et al. (2012) The toxin/immunity network of Burkholderia pseudomallei contact-dependent growth inhibition (CDI) systems. Mol Microbiol 84(3):516-529.
6. Aoki SK, Webb JS, Braaten BA, Low DA (2009) Contact-dependent growth inhibition causes reversible metabolic downregulation in Escherichia coli. J Bacteriol 191(6):1777-1786.
7. Diner EJ, Beck CM, Webb JS, Low DA, Hayes CS (2012) Identification of a target cell permissive factor required for contact-dependent growth inhibition (CDI). Genes Dev 26(5):515-525.
8. Poole SJ, et al. (2011) Identification of functional toxin/immunity genes linked to contact-dependent growth inhibition (CDI) and rearrangement hotspot (Rhs) systems. PLoS Genet 7(8):e1002217.
9. Holm L, Kääriäinen S, Rosenström P, Schenkel A (2008) Searching protein structure databases with DaliLite v.3. Bioinformatics 24(23):2780-2781. (Pubitemid 352722625)
10. Kachalova GS, et al. (2008) Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit. J Mol Biol 384(2):489-502.
11. Sokolowska M, Czapinska H, Bochtler M (2009) Crystal structure of the β β α-Me type II restriction endonuclease Hpy99I with target DNA. Nucleic Acids Res 37(11):3799-3810.
12. McGinness KE, Baker TA, Sauer RT (2006) Engineering controllable protein degradation. Mol Cell 22(5):701-707. (Pubitemid 43817606)
13. Yamaguchi Y, Park JH, Inouye M (2011) Toxin-antitoxin systems in bacteria and archaea. Annu Rev Genet 45:61-79.
14. Cascales E, et al. (2007) Colicin biology. Microbiol Mol Biol Rev 71(1):158-229. (Pubitemid 46456687)
15. Luna-Chávez C, Lin YL, Huang RH (2006) Molecular basis of inhibition of the ribonuclease activity in colicin E5 by its cognate immunity protein. J Mol Biol 358(2):571-579.
16. Graille M, Mora L, Buckingham RH, van Tilbeurgh H, de Zamaroczy M (2004) Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein. EMBO J 23(7):1474-1482. (Pubitemid 38579508)
17. Kleanthous C, et al. (1999) Structural and mechanistic basis of immunity toward endonuclease colicins. Nat Struct Biol 6(3):243-252. (Pubitemid 29107227)
18. Maté MJ, Kleanthous C (2004) Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases. J Biol Chem 279(33):34763-34769. (Pubitemid 39318108)
19. Ko TP, Liao CC, Ku WY, Chak KF, Yuan HS (1999) The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein. Structure 7(1):91-102.
20. Gronenborn AM (2009) Protein acrobatics in pairs: Dimerization via domain swapping. Curr Opin Struct Biol 19(1):39-49.
21. Yamasaki M, Li W, Johnson DJ, Huntington JA (2008) Crystal structure of a stable dimer reveals the molecular basis of serpin polymerization. Nature 455(7217):1255-1258.
22. Hillier BJ, Christopherson KS, Prehoda KE, Bredt DS, Lim WA (1999) Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex. Science 284(5415):812-815. (Pubitemid 29291348)
23. Housden NG, Loftus SR, Moore GR, James R, Kleanthous C (2005) Cell entry mechanism of enzymatic bacterial colicins: Porin recruitment and the thermodynamics of receptor binding. Proc Natl Acad Sci USA 102(39):13849-13854. (Pubitemid 41377667)
24. Loftus SR, et al. (2006) Competitive recruitment of the periplasmic translocation portal TolB by a natively disordered domain of colicin E9. Proc Natl Acad Sci USA 103(33):12353-12358. (Pubitemid 44267263)
25. Zhang D, Iyer LM, Aravind L (2011) A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Nucleic Acids Res 39(11):4532-4552.
26. Walker D, Lancaster L, James R, Kleanthous C (2004) Identification of the catalytic motif of the microbial ribosome inactivating cytotoxin colicin E3. Protein Sci 13(6):1603-1611. (Pubitemid 38669248)
27. Goulding CW, Perry LJ (2003) Protein production in Escherichia coli for structural studies by X-ray crystallography. J Struct Biol 142(1):133-143. (Pubitemid 36469246)
28. Goulding CW, et al. (2002) Crystal structure of a major secreted protein of Mycobacterium tuberculosis-MPT63 at 1.5-A resolution. Protein Sci 11(12):2887-2893. (Pubitemid 35365254)
29. Goulding CW, et al. (2002) Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD. Biochemistry 41(22):6920- 6927.
30. Niesen FH, Berglund H, Vedadi M (2007) The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc 2(9):2212-2221. (Pubitemid 351565860)