CdiA from Enterobacter Cloacae Delivers a Toxic Ribosomal RNase into Target Bacteria

Overview

Journal Structure

Publisher Cell Press

Specialties Biochemistry
Biotechnology
Cell Biology
Molecular Biology

Date 2014 Mar 25

PMID 24657090

Citations 52

Authors

Christina M Beck

Robert P Morse

David A Cunningham

Angelina Iniguez

David A Low

Celia W Goulding

Christopher S Hayes

Affiliations

Soon will be listed here.

Abstract

Contact-dependent growth inhibition (CDI) is one mechanism of inter-bacterial competition. CDI(+) cells export large CdiA effector proteins, which carry a variety of C-terminal toxin domains (CdiA-CT). CdiA-CT toxins are specifically neutralized by cognate CdiI immunity proteins to protect toxin-producing cells from autoinhibition. Here, we use structure determination to elucidate the activity of a CDI toxin from Enterobacter cloacae (ECL). The structure of CdiA-CT(ECL) resembles the C-terminal nuclease domain of colicin E3, which cleaves 16S ribosomal RNA to disrupt protein synthesis. In accord with this structural homology, we show that CdiA-CT(ECL) uses the same nuclease activity to inhibit bacterial growth. Surprisingly, although colicin E3 and CdiA(ECL) carry equivalent toxin domains, the corresponding immunity proteins are unrelated in sequence, structure, and toxin-binding site. Together, these findings reveal unexpected diversity among 16S rRNases and suggest that these nucleases are robust and versatile payloads for a variety of toxin-delivery platforms.

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References

Ruhe Z, Wallace A, Low D, Hayes C . Receptor polymorphism restricts contact-dependent growth inhibition to members of the same species. mBio. 2013; 4(4). PMC: 3735181. DOI: 10.1128/mBio.00480-13. View

Carr S, Walker D, James R, Kleanthous C, Hemmings A . Inhibition of a ribosome-inactivating ribonuclease: the crystal structure of the cytotoxic domain of colicin E3 in complex with its immunity protein. Structure. 2000; 8(9):949-60. DOI: 10.1016/s0969-2126(00)00186-6. View

Morse R, Nikolakakis K, Willett J, Gerrick E, Low D, Hayes C . Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems. Proc Natl Acad Sci U S A. 2012; 109(52):21480-5. PMC: 3535622. DOI: 10.1073/pnas.1216238110. View

Ogawa T, Tomita K, Ueda T, Watanabe K, Uozumi T, Masaki H . A cytotoxic ribonuclease targeting specific transfer RNA anticodons. Science. 1999; 283(5410):2097-100. DOI: 10.1126/science.283.5410.2097. View

Walker D, Lancaster L, James R, Kleanthous C . Identification of the catalytic motif of the microbial ribosome inactivating cytotoxin colicin E3. Protein Sci. 2004; 13(6):1603-11. PMC: 2279995. DOI: 10.1110/ps.04658504. View

Basturea G, Rudd K, Deutscher M . Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family. RNA. 2006; 12(3):426-34. PMC: 1383581. DOI: 10.1261/rna.2283106. View

Poole S, Diner E, Aoki S, Braaten B, tKint de Roodenbeke C, Low D . Identification of functional toxin/immunity genes linked to contact-dependent growth inhibition (CDI) and rearrangement hotspot (Rhs) systems. PLoS Genet. 2011; 7(8):e1002217. PMC: 3150448. DOI: 10.1371/journal.pgen.1002217. View

Rojas C, Ham J, Deng W, Doyle J, Collmer A . HecA, a member of a class of adhesins produced by diverse pathogenic bacteria, contributes to the attachment, aggregation, epidermal cell killing, and virulence phenotypes of Erwinia chrysanthemi EC16 on Nicotiana clevelandii seedlings. Proc Natl Acad Sci U S A. 2002; 99(20):13142-7. PMC: 130600. DOI: 10.1073/pnas.202358699. View

Hood R, Singh P, Hsu F, Guvener T, Carl M, Trinidad R . A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe. 2010; 7(1):25-37. PMC: 2831478. DOI: 10.1016/j.chom.2009.12.007. View

10.

Gite S, Reddy G, Shankar V . Active-site characterization of S1 nuclease. I. Affinity purification and influence of amino-group modification. Biochem J. 1992; 285 ( Pt 2):489-94. PMC: 1132814. DOI: 10.1042/bj2850489. View

11.

Pingoud A, Jeltsch A . Structure and function of type II restriction endonucleases. Nucleic Acids Res. 2001; 29(18):3705-27. PMC: 55916. DOI: 10.1093/nar/29.18.3705. View

12.

Riley M . Positive selection for colicin diversity in bacteria. Mol Biol Evol. 1993; 10(5):1048-59. DOI: 10.1093/oxfordjournals.molbev.a040054. View

13.

Rojas C, Ham J, Schechter L, Kim J, Beer S, Collmer A . The Erwinia chrysanthemi EC16 hrp/hrc gene cluster encodes an active Hrp type III secretion system that is flanked by virulence genes functionally unrelated to the Hrp system. Mol Plant Microbe Interact. 2004; 17(6):644-53. DOI: 10.1094/MPMI.2004.17.6.644. View

14.

MacIntyre D, Miyata S, Kitaoka M, Pukatzki S . The Vibrio cholerae type VI secretion system displays antimicrobial properties. Proc Natl Acad Sci U S A. 2010; 107(45):19520-4. PMC: 2984155. DOI: 10.1073/pnas.1012931107. View

15.

Holm L, Rosenstrom P . Dali server: conservation mapping in 3D. Nucleic Acids Res. 2010; 38(Web Server issue):W545-9. PMC: 2896194. DOI: 10.1093/nar/gkq366. View

16.

Ng C, Lang K, Meenan N, Sharma A, Kelley A, Kleanthous C . Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3. Nat Struct Mol Biol. 2010; 17(10):1241-1246. PMC: 3755339. DOI: 10.1038/nsmb.1896. View

17.

Koskiniemi S, Lamoureux J, Nikolakakis K, tKint de Roodenbeke C, Kaplan M, Low D . Rhs proteins from diverse bacteria mediate intercellular competition. Proc Natl Acad Sci U S A. 2013; 110(17):7032-7. PMC: 3637788. DOI: 10.1073/pnas.1300627110. View

18.

Diner E, Beck C, Webb J, Low D, Hayes C . Identification of a target cell permissive factor required for contact-dependent growth inhibition (CDI). Genes Dev. 2012; 26(5):515-25. PMC: 3305988. DOI: 10.1101/gad.182345.111. View

19.

Czaran T, Hoekstra R, Pagie L . Chemical warfare between microbes promotes biodiversity. Proc Natl Acad Sci U S A. 2002; 99(2):786-90. PMC: 117383. DOI: 10.1073/pnas.012399899. View

20.

Diner E, Hayes C . Recombineering reveals a diverse collection of ribosomal proteins L4 and L22 that confer resistance to macrolide antibiotics. J Mol Biol. 2009; 386(2):300-15. PMC: 2644216. DOI: 10.1016/j.jmb.2008.12.064. View