Reconstitution and Structure of a Bacterial Pnkp1-Rnl-Hen1 RNA Repair Complex

Overview

Journal Nat Commun

Specialty Biology

Date 2015 Apr 18

PMID 25882814

Citations 9

Authors

Pei Wang

Kiruthika Selvadurai

Raven H Huang

Affiliations

Soon will be listed here.

Abstract

Ribotoxins cleave essential RNAs for cell killing, and RNA repair neutralizes the damage inflicted by ribotoxins for cell survival. Here we report a new bacterial RNA repair complex that performs RNA repair linked to immunity. This new RNA repair complex is a 270-kDa heterohexamer composed of three proteins-Pnkp1, Rnl and Hen1-that are required to repair ribotoxin-cleaved RNA in vitro. The crystal structure of the complex reveals the molecular architecture of the heterohexamer as two rhomboid-shaped ring structures of Pnkp1-Rnl-Hen1 heterotrimer fused at the Pnkp1 dimer interface. The four active sites required for RNA repair are located on the inner rim of each ring. The architecture and the locations of the active sites of the Pnkp1-Rnl-Hen1 heterohexamer suggest an ordered series of repair reactions at the broken RNA ends that confer immunity to recurrent damage.

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References

Nariya H, Inouye M . MazF, an mRNA interferase, mediates programmed cell death during multicellular Myxococcus development. Cell. 2008; 132(1):55-66. DOI: 10.1016/j.cell.2007.11.044. View

Leplae R, Geeraerts D, Hallez R, Guglielmini J, Dreze P, Van Melderen L . Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families. Nucleic Acids Res. 2011; 39(13):5513-25. PMC: 3141249. DOI: 10.1093/nar/gkr131. View

Chakravarty A, Smith P, Jalan R, Shuman S . Structure, mechanism, and specificity of a eukaryal tRNA restriction enzyme involved in self-nonself discrimination. Cell Rep. 2014; 7(2):339-347. PMC: 4121121. DOI: 10.1016/j.celrep.2014.03.034. View

Zhang C, Chan C, Wang P, Huang R . Probing the substrate specificity of the bacterial Pnkp/Hen1 RNA repair system using synthetic RNAs. RNA. 2011; 18(2):335-44. PMC: 3264919. DOI: 10.1261/rna.030502.111. View

Smith P, Wang L, Nair P, Shuman S . The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family. Proc Natl Acad Sci U S A. 2012; 109(7):2296-301. PMC: 3289333. DOI: 10.1073/pnas.1116827109. View

Otwinowski Z, Minor W . Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997; 276:307-26. DOI: 10.1016/S0076-6879(97)76066-X. View

Holm L, Kaariainen S, Rosenstrom P, Schenkel A . Searching protein structure databases with DaliLite v.3. Bioinformatics. 2008; 24(23):2780-1. PMC: 2639270. DOI: 10.1093/bioinformatics/btn507. View

Cook G, Robson J, Frampton R, McKenzie J, Przybilski R, Fineran P . Ribonucleases in bacterial toxin-antitoxin systems. Biochim Biophys Acta. 2013; 1829(6-7):523-31. DOI: 10.1016/j.bbagrm.2013.02.007. View

Pedersen K, Zavialov A, Pavlov M, Elf J, Gerdes K, Ehrenberg M . The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell. 2003; 112(1):131-40. DOI: 10.1016/s0092-8674(02)01248-5. View

10.

Tomita K, Ogawa T, Uozumi T, Watanabe K, Masaki H . A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops. Proc Natl Acad Sci U S A. 2000; 97(15):8278-83. PMC: 26938. DOI: 10.1073/pnas.140213797. View

11.

Chan C, Zhou C, Huang R . Reconstituting bacterial RNA repair and modification in vitro. Science. 2009; 326(5950):247. DOI: 10.1126/science.1179480. View

12.

Neubauer C, Gao Y, Andersen K, Dunham C, Kelley A, Hentschel J . The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE. Cell. 2009; 139(6):1084-95. PMC: 2807027. DOI: 10.1016/j.cell.2009.11.015. View

13.

Garces F, Pearl L, Oliver A . The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase. Mol Cell. 2011; 44(3):385-96. PMC: 4820033. DOI: 10.1016/j.molcel.2011.08.036. View

14.

Zhang D, de Souza R, Anantharaman V, Iyer L, Aravind L . Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct. 2012; 7:18. PMC: 3482391. DOI: 10.1186/1745-6150-7-18. View

15.

Galburt E, Pelletier J, Wilson G, Stoddard B . Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase. Structure. 2002; 10(9):1249-60. DOI: 10.1016/s0969-2126(02)00835-3. View

16.

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

17.

Amitsur M, Levitz R, Kaufmann G . Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J. 1987; 6(8):2499-503. PMC: 553660. DOI: 10.1002/j.1460-2075.1987.tb02532.x. View

18.

Huang Y, Ji L, Huang Q, Vassylyev D, Chen X, Ma J . Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature. 2009; 461(7265):823-7. PMC: 5125239. DOI: 10.1038/nature08433. View

19.

Teles R, Bogren A, Patel M, Wennstrom J, Socransky S, Haffajee A . A three-year prospective study of adult subjects with gingivitis II: microbiological parameters. J Clin Periodontol. 2007; 34(1):7-17. DOI: 10.1111/j.1600-051X.2006.01015.x. View

20.

Morad I, Amitsur M, Kaufmann G . Functional expression and properties of the tRNA(Lys)-specific core anticodon nuclease encoded by Escherichia coli prrC. J Biol Chem. 1993; 268(36):26842-9. View