Insertion of group II intron-based ribozyme switches into homing endonuclease genes

Methods in Molecular Biology

Volumn 1498, Issue , 2017, Pages 135-152

  Guha, Tuhin Kumar ^a   Hausner, Georg ^a  

^a UNIVERSITY OF MANITOBA   (Canada)

Author keywords

Biotechnology; Group II introns; Homing endonuclease assay; Homing endonucleases; Targeted mutagenesis; Temporal regulation

Indexed keywords

BACTERIAL RNA; COBALT CHLORIDE; COMPLEMENTARY DNA; EDETIC ACID; ENDONUCLEASE; GLUCOSE; HOMING ENDONUCLEASE; KANAMYCIN; MAGNESIUM CHLORIDE; PLASMID DNA; UNCLASSIFIED DRUG; MITOCHONDRIAL DNA; RIBOZYME;

AGAR GEL ELECTROPHORESIS; ALLELE; AMPLICON; BACTERIAL CELL; BINDING SITE; CENTRIFUGATION; CONFERENCE PAPER; CULTURE MEDIUM; ENZYME ACTIVITY; ENZYME PURIFICATION; ESCHERICHIA COLI; EXON; EXPRESSION VECTOR; GENE OVEREXPRESSION; GENE SYNTHESIS; GROUP II INTRON; INTRON; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RIBOSWITCH; RNA CLEAVAGE; RNA SPLICING; START CODON; GENETICS;

DNA, MITOCHONDRIAL; ENDONUCLEASES; ESCHERICHIA COLI; INTRONS; OPEN READING FRAMES; RNA SPLICING; RNA, CATALYTIC;

EID: 84990966965     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-6472-7_9     Document Type: Conference Paper

References (34)

1. Stoddard BL (2006) Homing endonuclease structure and function. Q Rev Biophys 38:49–95
2. Gimble FS (2000) Invasion of a multitude of genetic niches by mobile endonuclease genes. FEMS Microbiol Lett 185:99–107
3. Hausner G (2012) Introns, mobile elements and plasmids. In: Bullerwell CE (ed) Organelle genetics: evolution of organelle genomes and gene expression. Springer, Berlin, pp 101–131
4. Liu JK, Chen WH, Ren SX, Zhao GP, Wang J (2014) iBrick: a new standard for iterative assembly of biological parts with homing endonucleases. PLoS One 9:e110852
5. Stoddard BL, Scharenberg AM, Monnat RJ Jr (2008) Advances in engineering homing endonucleases for gene targeting: ten years after structures. In: Bertolotti R, Ozawa K (eds) Progress in gene therapy 3: autologous and cancer stem cell gene therapy. World Scientific Press, Hackensack, NJ, pp 135–167
6. Marcaid MJ, Muñoz IG, Blanco FJ, Prieto J, Montoya G (2010) Homing endonucleases: from basics to therapeutic applications. Cell Mol Life Sci 67:727–748
7. Takeuchi R, Lambert AR, Mak AN, Jacoby K, Dickson RJ, Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL (2011) Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proc Natl Acad Sci U S A 108:13077–13082
8. Stoddard BL (2011) Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification. Structure 19:7–15
9. Hafez M, Hausner G (2012) Homing endonucleases: DNA scissors on a mission. Genome 55:553–569
10. Prieto J, Molina R, Montoya G (2012) Molecular scissors for in situ cellular repair. Crit Rev Biochem Mol Biol 47:207–221
11. Posey KL, Gimble FS (2002) Insertion of reversible redox switch into a rare cutting DNA endonuclease. Biochemistry 41:2184–2190
12. Olga F, Nora Z (2007) Group II introns: structure, folding and splicing mechanism. Biol Chem 388:665–678
13. Michel F, Costa M, Westhof E (2009) The ribozyme core of group II introns: a structure in want of partners (Review). Trends Biochem Sci 34:189–199
14. Donghi D, Pechlaner M, Finazzo C, Knobloch B, Sigel RKO (2013) The structural stabilization of the ? three-way junction by Mg(II) represents the first step in the folding of a group II intron. Nucleic Acids Res 41:2489–2504
15. Sigel RKO (2005) Group II intron ribozymes and metal ions—a delicate relationship. Eur J Inorg Chem 12:2281–2292
16. Lambowitz AM, Belfort M (2015) Mobile bacterial group II introns at the crux of eukaryotic evolution. Microbiol Spectr 3:MDNA3-0050-2014
17. Puigbò P, Guzmán E, Romeu A, Garcia-Vallvé S (2007) OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res 35:W126–W131
18. Hirose S, Noguchi T (2013) ESPRESSO: a system for estimating protein expression and solubility in protein expression systems. Proteomics 13:1444–1456
19. Toor N, Hausner G, Zimmerly S (2001) Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 8:1142–1152
20. Lambowitz AM, Zimmerly S (2004) Mobile group II introns. Annu Rev Genet 38:1–35
21. Lambowitz AM, Zimmerly S (2011) Group II introns: mobile ribozymes that invade DNA. Cold Spring Harb Perspect Biol 3:a003616
22. Hafez M, Majer A, Sethuraman J, Rudski SM, Michel F, Hausner G (2013) The mtDNA rns gene landscape in Ophiostomatales and other fungal taxa: twintrons, introns and intron encoded proteins. Fungal Genet Biol 53:71–83
23. Guha TK, Hausner G (2014) A homing endonuclease with a switch: characterization of a twintron encoded homing endonuclease. Fungal Genet Biol 65:57–68
24. Kück U, Godehardt I, Schmidt U (1990) A self-splicing group II intron in the mitochondrial large subunit rRNA (LSUrRNA) gene of the eukaryotic alga Scenedesmus obliquus. Nucleic Acids Res 18:2691–2697
25. Hollander V, Kück U (1999) Group II intron splicing in Escherichia coli: phenotypes of cis-acting mutations resemble splicing defects observed in organelle RNA processing. Nucleic Acids Res 27:2339–2344
26. Candales MA, Duong A, Hood KS, Li T, Neufeld RA, Sun R, McNeil BA, Wu L, Jarding AM, Zimmerly S (2012) Database for bacterial group II introns. Nucleic Acids Res 40(Database issue):D187–D190
27. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D’Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3:2
28. Green MR, Sambrook R (2012) Molecular cloning, a laboratory manual, 4th edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
29. Dafa’alla TH, Hobom G, Zahner H (2000) Direct colony identification by PCR-Miniprep. Mol Biol Today 1:65–66
30. Bae H, Kim KP, Song JM, Kim JH, Yang JS, Kwon ST (2009) Characterization of intein homing endonuclease encoded in the DNA polymerase gene of Thermococcus marinus. FEMS Microbiol Lett 297:180–188
31. Nelson DL, Kennedy EP (1971) Magnesium transport in Escherichia coli. Inhibition by cobaltous ion. J Biol Chem 246:3042–3049
32. Nelson DL, Kennedy EP (1972) Transport of magnesium by a repressible and a nonrepressible system in Escherichia coli. Proc Natl Acad Sci U S A 69:1091–1093
33. Hafez M, Guha TK, Shen C, Sethuraman J, Hausner G (2014) PCR-based bioprospecting for homing endonucleases in fungal mitochondrial rRNA genes. Methods Mol Biol 1123:37–53
34. Taylor GK, Petrucci LH, Lambert AR, Baxter SK, Jarjour J, Stoddard BL (2012) LAHEDES: the LAGLIDADG homing endonuclease database and engineering server. Nucleic Acids Res 40(Web Server issue):W110–W116