Preparation of group I introns for biochemical studies and crystallization assays by native affinity purification

PLoS ONE

Volumn 4, Issue 8, 2009, Pages

  Vicens, Quentin ^a   Gooding, Anne R ^a   Duarte, Luis F ^b   Batey, Robert T ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; NUCLEOTIDE;

ARTICLE; CHEMICAL ANALYSIS; CLOSTRIDIUM BOTULINUM; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; DNA DENATURATION; EXON; GEL ELECTROPHORESIS; GROUP I INTRON; INTRON; ISOLATION PROCEDURE; ISOTOPE LABELING; NATIVE AFFINITY PURIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA CLEAVAGE; RNA PURIFICATION; RNA SPLICING; RNA STRUCTURE; STRUCTURE ANALYSIS; AFFINITY CHROMATOGRAPHY; BACTERIAL GENE; CHEMISTRY; CONFORMATION; GENETIC TRANSCRIPTION; GENETICS; METHODOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS; X RAY CRYSTALLOGRAPHY;

CLOSTRIDIUM BOTULINUM;

BASE SEQUENCE; CHROMATOGRAPHY, AFFINITY; CLOSTRIDIUM BOTULINUM; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; EXONS; GENES, BACTERIAL; INTRONS; NUCLEIC ACID CONFORMATION; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; TRANSCRIPTION, GENETIC;

EID: 69449104554     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006740     Document Type: Article

References (40)

1. Gesteland RF, Cech TR, Atkins JF (2006) The RNA World - Third edition; Gesteland RF, Cech TR, Atkins JF, eds. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
2. Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 15 Spec No 1: R17-29.
3. Kieft JS, Batey RT (2004) A general method for rapid and nondenaturing purification of RNAs. RNA 10: 988-995.
4. Perrotta AT, Shih I, Been MD (1999) Imidazole Rescue of a Cytosine Mutation in a Self-Cleaving Ribozyme. Science 286: 123-126.
5. Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA (2000) Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287: 1232-1239.
6. Batey RT, Gilbert SD, Montange RK (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432: 411-415.
7. Dann CE, 3rd, Wakeman CA, Sieling CL, Baker SC, Irnov I, et al. (2007) Structure and mechanism of a metal-sensing regulatory RNA. Cell 130: 878-892.
8. Batey RT, Kieft JS (2007) Improved native affinity purification of RNA. RNA 13: 1384-1389.
9. Kuhsel MG, Strickland R, Palmer JD (1990) An ancient group I intron shared by eubacteria and chloroplasts. Science 250: 1570-1573.
10. Williams KP (2002) The tmRNA Website: invasion by an intron. Nucleic Acids Res 30: 179-182.
11. Xu MQ, Kathe SD, Goodrich-Blair H, Nierzwicki-Bauer SA, Shub DA (1990) Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria. Science 250: 1566-1570.
12. Machouart-Dubach M, Lacroix C, Vaury C, Feuilhade de Chauvin M, Bellanne C, et al. (2002) Nucleotide structure of the Scytalidium hyalinum and Scytalidium dimidiatum 18S subunit ribosomal RNA gene: evidence for the insertion of a group IE intron in the rDNA gene of S. dimidiatum. FEMS Microbiol Lett 208: 187-196.
13. Chu FK, Maley GF, West DK, Belfort M, Maley F (1986) Characterization of the intron in the phage T4 thymidylate synthase gene and evidence for its self-excision from the primary transcript. Cell 45: 157-166.
14. Heilman-Miller SL, Woodson SA (2003) Perturbed folding kinetics of circularly permuted RNAs with altered topology. J Mol Biol 328: 385-394.
15. Puttaraju M, Been MD (1992) Group I permuted intron-exon (PIE) sequences self-splice to produce circular exons. Nucleic Acids Res 20: 5357-5364.
16. Horton RM, Hunt HD, Ho SN, Pullen JK, Pease LR (1989) Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77: 61-68.
17. Bryan TM, Goodrich KJ, Cech TR (2000) A mutant of Tetrahymena telomerase reverse transcriptase with increased processivity. J Biol Chem 275: 24199-24207.
18. Ferre-D'Amare AR, Zhou K, Doudna JA (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature 395: 567-574.
19. Rosenstein SP, Been MD (1996) Hepatitis delta virus ribozymes fold to generate a solvent-inaccessible core with essential nucleotides near the cleavage site phosphate. Biochemistry 35: 11403-11413.
20. Pichler A, Schroeder R (2002) Folding problems of the 59 splice site containing the P1 stem of the group I thymidylate synthase intron: substrate binding inhibition in vitro and mis-splicing in vivo. J Biol Chem 277: 17987-17993.
21. Adams PL, Stahley MR, Gill ML, Kosek AB, Wang J, et al. (2004) Crystal structure of a group I intron splicing intermediate. RNA 10: 1867-1887.
22. Chase E, Golden BL (2005) Crystallization and preliminary diffraction analysis of a group I ribozyme from bacteriophage Twort. Acta Cryst F61: 71-74.
23. Vicens Q, Paukstelis PJ, Westhof E, Lambowitz AM, Cech TR (2008) Toward predicting self-splicing and protein-facilitated splicing of group I introns. RNA 14: 2013-2029.
24. Doudna JA, Grosshans C, Gooding A, Kundrot CE (1993) Crystallization of ribozymes and small RNA motifs by a sparse matrix approach. Proc Natl Acad Sci USA 90: 7829-7833.
25. Golden BL, Kundrot CE (2003) RNA crystallization. J Struct Biol 142: 98-107.
26. Hansen CL, Skordalakes E, Berger JM, Quake SR (2002) A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion. Proc Natl Acad Sci USA 99: 16531-16536.
27. Hanson BL, Schall CA, Bunick GJ (2003) New techniques in macromolecular cryocrystallography: macromolecular crystal annealing and cryogenic helium. J Struct Biol 142: 77-87.
28. Kriminski S, Caylor CL, Nonato MC, Finkelstein KD, Thorne RE (2002) Flash-cooling and annealing of protein crystals. Acta Cryst D58: 459-471.
29. Edwards AL, Garst AD, Batey RT (2009) Determining structures of RNA aptamers and riboswitches by X-ray crystallography. Methods Mol Biol 535: 135-163.
30. Juneau K, Podell E, Harrington DJ, Cech TR (2001) Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions. Structure 9: 221-231.
31. Michel F, Ellington AD, Couture S, Szostak JW (1990) Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature 347: 578-580.
32. Ehrenman K, Schroeder R, Chandry PS, Hall DH, Belfort M (1989) Sequence specificity of the P6 pairing for splicing of the group I td intron of phage T4. Nucleic Acids Res 17: 9147-9163.
33. Belfort M, Chandry PS, Pedersen-Lane J (1987) Genetic delineation of functional components of the group I intron in the phage T4 td gene. Cold Spring Harb Symp Quant Biol 52: 181-192.
34. Chen X, Gutell RR, Lambowitz AM (2000) Function of tyrosyl-tRNA synthetase in splicing group I introns: an induced-fit model for binding to the P4-P6 domain based on analysis of mutations at the junction of the P4-P6 stacked helices. J Mol Biol 301: 265-283.
35. Mohr G, Zhang A, Gianelos JA, Belfort M, Lambowitz AM (1992) The Neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core. Cell 69: 483-494.
36. Waldsich C, Grossberger R, Schroeder R (2002) RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo. Genes Dev 16: 2300-2312.
37. Galloway Salvo JL, Coetzee T, Belfort M (1990) Deletion-tolerance and trans-splicing of the bacteriophage T4 td intron. Analysis of the P6-L6a region. J Mol Biol 211: 537-549.
38. Zaug AJ, McEvoy MM, Cech TR (1993) Self-splicing of the group I intron from Anabaena pre-tRNA: requirement for base-pairing of the exons in the anticodon stem. Biochemistry 32: 7946-7953.
39. Powell HR (1999) The Rossmann Fourier autoindexing algorithm in MOSFLM. Acta Cryst D55: 1690-1695.
40. Leontis NB, Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7: 499-512.