Reactions of Cre with methylphosphonate DNA: Similarities and contrasts with Flp and vaccinia topoisomerase

PLoS ONE

Volumn 4, Issue 9, 2009, Pages

  Ma, Chien Hui ^a   Kachroo, Aashiq H ^a   Macieszak, Anna ^b   Chen, Tzu Yang ^a   Guga, Piotr ^b   Jayaram, Makkuni ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b CENTRE OF MOLECULAR AND MACROMOLECULAR STUDIES   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; CRE RECOMBINASE; DNA; DNA TOPOISOMERASE; OLIGODEOXYRIBONUCLEOSIDE METHYLPHOSPHONATE; RECOMBINASE; TYROSINE; WATER; ALANINE; DNA POLYMERASE; INTEGRASE; PHOSPHONIC ACID DERIVATIVE;

ARTICLE; DNA CLEAVAGE; DNA RECOMBINATION; DNA STRAND; ELECTRICITY; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; GENETIC COMPLEMENTATION; GENETIC CONSERVATION; GENETIC DAMAGE; HYDROLYSIS; RNA PROCESSING; TRANSESTERIFICATION; BIOLOGICAL MODEL; CHEMISTRY; ENZYMOLOGY; ESCHERICHIA COLI; GENETIC VARIABILITY; METABOLISM; STATIC ELECTRICITY; VACCINIA VIRUS;

ALANINE; ARGININE; CATALYTIC DOMAIN; DNA; DNA NUCLEOTIDYLTRANSFERASES; DNA TOPOISOMERASES; ESCHERICHIA COLI; GENETIC VARIATION; HYDROLYSIS; INTEGRASES; MODELS, BIOLOGICAL; PHOSPHONIC ACIDS; STATIC ELECTRICITY; TYROSINE; VACCINIA VIRUS;

EID: 70349687018     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007248     Document Type: Article

References (33)

1. Jayaram M, Mehta S, Uzri D, Voziyanov Y, Velmurugan S (2004) Site-specific recombination and partitioning systems in the stable high copy propagation of the 2-micron yeast plasmid. In: Moldave K. ed. Prog Nucl Acid Res Mol Biol: Academic Press. Vol 77: pp 127-172.
2. Jayaram M, Tribble G, Grainge I, editors (2002) Site-specific recombination by the Flp protein of Saccharomyces cerevisiae. In: Craig NL, Craigie R, Gellert M, Lambowitz AM, eds. Mobile DNA II. Washington DC: ASM Press. pp 192-218.
3. Van Duyne GD (2002) A structural view of tyrosine recombinase site-specific recombination. In: Craig NL, Craigie R, Gellert M, Lambowitz AM, eds. Mobile DNA II. Washington DC: ASM Press. pp 93-117.
4. Rice PA (2002) Theme and variation in tyrosine recombinases: structure of a Flp-DNA complex; In: Craig NL, Craigie R, Gellert M, Lambowitz AM, eds. Mobile DNA II. Washington DC: ASM Press. pp 219-229.
5. Chen Y, Narendra U, Iype LE, Cox MM, Rice PA (2000) Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping. Mol Cell 6: 885-897.
6. Guo F, Gopaul DN, Van Duyne GD (1997) Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 389: 40-46.
7. Krogh BO, Shuman S (2000) Catalytic mechanism of DNA topoisomerase IB. Mol Cell 5: 1035-1041.
8. Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG (1998) Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 279: 1504-1513.
9. Chen Y, Rice PA (2003) The role of the conserved Trp330 in Flp-mediated recombination: functional and structural analysis. J Biol Chem 278: 24800-24807.
10. Mizuuchi K (1997) Polynucleotidyl transfer reactions in site-specific DNA recombination. Genes Cells 2: 1-12.
11. Mizuuchi K, Baker TA (2002) Chemical mechanisms for mobilizing DNA. In: Craig NL, Craigie R, Gellert M, Lambowitz AM, eds. Mobile DNA II. Washington DC: ASM Press. pp 12-23.
12. An S, Barany G, Musier-Forsyth K (2008) Evolution of acceptor stem tRNA recognition by class II prolyl-tRNA synthetase. Nucleic Acids Res 36: 2514-2521.
13. Dash C, Scarth BJ, Badorrek C, Gotte M, Le Grice SF (2008) Examining the ribonuclease H primer grip of HIV-1 reverse transcriptase by charge neutralization of RNA/DNA hybrids. Nucleic Acids Res 36: 6363-6371.
14. Dertinger D, Uhlenbeck OC (2001) Evaluation of methylphosphonates as analogs for detecting phosphate contacts in RNA-protein complexes. RNA 7: 622-631.
15. Noble SA, Fisher EF, Caruthers MH (1984) Methylphosphonates as probes of protein-nucleic acid interactions. Nucleic Acids Res 12: 3387-3404.
16. Parker JB, Stivers JT (2008) Uracil DNA glycosylase: revisiting substrate-assisted catalysis by DNA phosphate anions. Biochemistry 47: 8614-8622.
17. Pritchard CE, Grasby JA, Hamy F, Zacharek AM, Singh M, et al. (1994) Methylphosphonate mapping of phosphate contacts critical for RNA recognition by the human immunodeficiency virus tat and rev proteins. Nucleic Acids Res 22: 2592-2600.
18. Rosati O, Srivastava TK, Katti SB, Alves J (2002) Importance of phosphate contacts for sequence recognition by EcoRI restriction enzyme. Biochem Biophys Res Commun 295: 198-205.
19. Ma CH, Rowley PA, Maciaszek A, Guga P, Jayaram M (2009) Active site electrostatics protect genome integrity by blocking abortive hydrolysis during DNA recombination. EMBO J 28: 1745-1756.
20. Tian L, Claeboe CD, Hecht SM, Shuman S (2005) Mechanistic plasticity of DNA topoisomerase IB: phosphate electrostatics dictate the need for a catalytic arginine. Structure 13: 513-520.
21. Tian L, Claeboe CD, Hecht SM, Shuman S (2003) Guarding the genome: electrostatic repulsion of water by DNA suppresses a potent nuclease activity of topoisomerase IB. Mol Cell 12: 199-208.
22. Belfort M, Derbyshire V, Parker MM, Cousineau B, Lambowitz AM (2002) Mobile introns: pathways and proteins. In: Craig NL, Craigie R, Gellert M, Lambowitz AM, eds. Mobile DNA II. Washington DC: ASM Press. pp 761-783.
23. Cech TR (1983) RNA splicing: three themes with variations. Cell 34: 713-716.
24. Craig NL (2002) Mobile DNA: an introduction; In: Craig NL, Craigie R, Gellert M, Lambowitz AM, eds. Mobile DNA II. Washington DC: ASM Press. pp 3-11.
25. Woods KC, Martin SS, Chu VC, Baldwin EP (2001) Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction. J Mol Biol 313: 49-69.
26. Ghosh K, Van Duyne GD (2002) Cre-loxP biochemistry. Methods 28: 374-383.
27. Agarwal KL, Riftina F (1979) Synthesis and enzymatic properties of deoxyribooligonucleotides containing methyl and phenylphosphonate linkages. Nucleic Acids Res 6: 3009-3024.
28. Sau AK, DeVue Tribble G, Grainge I, Frohlich RF, Knudsen BR, et al. (2001) Biochemical and kinetic analysis of the RNase active sites of the integrase/tyrosine family site-specific DNA recombinases. J Biol Chem 276: 46612-46623.
29. Xu C-J, Grainge I, Lee J, Harshey RM, Jayaram M (1998) Unveiling two distinct ribonuclease activities and a topoisomerase activity in a site-specific DNA recombinase. Mol Cell 1: 729-739.
30. Lee J, Jayaram M (1993) Mechanism of site-specific recombination. Logic of assembling recombinase catalytic site from fractional active sites. J Biol Chem 268: 17564-17570.
31. Conway AB, Chen Y, Rice PA (2003) Structural plasticity of the Flp-Holliday junction complex. J Mol Biol 326: 425-434.
32. Lee J, Whang I, Jayaram M (1996) Assembly and orientation of Flp recombinase active sites on two-, three- and four-armed DNA substrates: implications for a recombination mechanism. J Mol Biol 257: 532-549.
33. Shaikh AC, Sadowski PD (1997) The Cre recombinase cleaves the lox site in trans. J Biol Chem 272: 5695-5702.