Involvement of Vts1, a structure-specific RNA-binding protein, in Okazaki fragment processing in yeast

Nucleic Acids Research

Volumn 38, Issue 5, 2009, Pages 1583-1595

  Lee, Chul Hwan ^a   Shin, Yong Keol ^a   Phung, Thi Thu Huong ^a   Bae, Jae Seok ^a   Kang, Young Hoon ^a   Nguyen, Tuan Anh ^a   Kim, Jeong Hoon ^a   Kim, Do Hyung ^a   Kang, Min Jung ^a   Bae, Sung Ho ^b   Seo, Yeon Soo ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b Inha University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ASPARAGINE; DEOXYRIBONUCLEASE; DNA; GLUTAMIC ACID; HELICASE; LYSINE; OKAZAKI FRAGMENT; PROTEIN VTS1; RECOMBINANT PROTEIN; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; DNA2 PROTEIN, S CEREVISIAE; FLAP ENDONUCLEASE; OKAZAKI FRAGMENTS; RAD27 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; VTS1 PROTEIN, S CEREVISIAE;

ALLELE; AMINO TERMINAL SEQUENCE; ARTICLE; CELL GROWTH; CELL MUTANT; CONTROLLED STUDY; DNA SYNTHESIS; ENZYME ACTIVATION; ENZYME ACTIVITY; FUNGAL STRAIN; GENE OVEREXPRESSION; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; TEMPERATURE DEPENDENCE; TRANSCRIPTION REGULATION; CELL NUCLEUS; CHEMISTRY; ENZYMOLOGY; GENE REPRESSION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MUTATION;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

ALLELES; CELL NUCLEUS; DNA; DNA HELICASES; DNA-BINDING PROTEINS; ENDODEOXYRIBONUCLEASES; FLAP ENDONUCLEASES; MUTATION; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SUPPRESSION, GENETIC;

EID: 77950506185     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1135     Document Type: Article

References (33)

1. MacNeill,S.A. (2001) DNA replication: partners in the Okazaki two-step. Curr. Biol., 11, R842-R844.
2. Hübscher,U. and Seo,Y.S. (2001) Replication of the lagging strand: a concert of at least 23 polypeptides. Mol. Cells, 12, 149-157.
3. Liu,Y., Kao,H.I. and Bambara,R.A. (2004) Flap endonuclease 1: a central component of DNA metabolism. Annu. Rev. Biochem., 73, 589-615.
4. Garg,P. and Burgers,P.M. (2005) DNA polymerases that propagate the eukaryotic DNA replication fork. Crit. Rev. Biochem. Mol. Biol., 40, 115-128.
5. Rossi,M.L., Purohit,V., Brandt,P.D. and Bambara,R.A. (2006) Lagging strand replication proteins in genome stability and DNA repair. Chem. Rev., 106, 453-473.
6. Denis,D. and Bullock,P.A. (1993) Primer-DNA formation during simian virus 40 DNA replication in vitro. Mol. Cell. Biol., 13, 2882-2890.
7. Tsurimoto,T. and Stillman,B. (1991) Replication factors required for SV40 DNA replication in vitro: II. Switching of DNA polymerase alpha and delta during initiation of leading and lagging strand synthesis. J. Biol. Chem., 266, 1961-1968.
8. Bae,S.H. and Seo,Y.S. (2000) Characterization of the enzymatic properties of the yeast dna2 Helicase/endonuclease suggests a new model for Okazaki fragment processing. J. Biol. Chem., 275, 38022-38031.
9. Bae,S.H., Kim,J.A., Choi,E., Lee,K.H., Kang,H.Y., Kim,H.D., Kim,J.H., Bae,K.H., Cho,Y., Park,C. et al. (2001b) Tripartite structure of Saccharomyces cerevisiae Dna2 helicase/endonuclease. Nucleic Acids Res., 29, 3069-3079.
10. Ayyagari,R., Gomes,X.V., Gordenin,D.A. and Burgers,P.M. (2003) Okazaki fragment maturation in yeast: I. Distribution of functions between FEN1 AND DNA2. J. Biol. Chem., 278, 1618-1625.
11. Rossi,M.L. and Bambara,R.A. (2006) Reconstituted Okazaki fragment processing indicates two pathways of primer removal. J. Biol. Chem., 281, 26051-26061.
12. Harrington,J.J. and Lieber,M.R. (1994) Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair. Genes Dev., 8, 1344-1355.
13. Bae,S.H., Bae,K.H., Kim,J.A. and Seo,Y.S. (2001) RPA governs endonuclease switching during processing of Okazaki fragments in eukaryotes. Nature, 412, 456-461.
14. Pike,J.E., Burgers,P.M., Campbell,J.L. and Bambara,R.A. (2009) Pif1 helicase lengthens some Okazaki fragment flaps necessitating Dna2 nuclease/helicase action in the two-nuclease processing pathway. J. Biol. Chem., 284, 25170-25180.
15. Jin,Y.H., Ayyagari,R., Resnick,M.A., Gordenin,D.A. and Burgers,P.M. (2003) Okazaki fragment maturation in yeast II: cooperation between the polymerase δ and 3′ to 5′ exonuclease activities of pol d in the creation of a ligatable nick. J. Biol. Chem., 278, 1626-1633.
16. Budd,M.E., Choe,W.C. and Campbell,J.L. (1995) DNA2 encodes a DNA helicase essential for replication of eukaryotic chromosomes. J. Biol. Chem., 270, 26766-26769.
17. Bae,S.H., Choi,E., Lee,K.H., Park,J.S., Lee,S.H. and Seo,Y.S. (1998) Dna2 of Saccharomyces cerevisiae possesses a single-stranded DNA-specific endonuclease activity that is able to act on double-stranded DNA in the presence of ATP. J. Biol. Chem., 273, 26880-26890.
18. Bae,S.H., Kim,D.W., Kim,J., Kim,J.H., Kim,D.H., Kim,H.D., Kang,H.Y. and Seo,Y.S. (2002) Coupling of DNA helicase and endonuclease activities of yeast Dna2 facilitates Okazaki fragment processing. J. Biol. Chem., 277, 26632-26641.
19. Dilcher,M., Kohler,B. and von Mollard,G.F. (2001) Genetic interactions with the yeast Q-SNARE VTI1 reveal novel functions for the R-SNARE YKT6. J. Biol. Chem., 276, 34537-34544.
20. Hall,T.M. (2003) SAM breaks its sterotype. Nat. Struct. Biol., 10, 677-679.
21. Qiao,F. and Bowie,J.U. (2005) The many faces of SAM. Sci. STKE, 2005, re7.
22. Aviv,T., Lin,Z., Lau,S., Rendl,L.M., Sicheri,F. and Smibert,C.A. (2003) The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. Nat. Struct. Biol., 10, 614-621.
23. Green,J.B., Gardner,C.D., Wharton,R.P. and Aggarwal,A.K. (2003) RNA recognition via the SAM domain of Smaug. Mol. Cell., 11, 1537-1548.
24. Edwards,T.A., Butterwick,J.A., Zeng,L., Gupta,Y.K., Wang,X., Wharton,R.P., Palmer,A.G. 3rd and Aggarwal,A.K. (2006) Solution structure of the Vts1 SAM domain in the presence of RNA. J. Mol. Biol., 356, 1065-1072.
25. Johnson,P.E. and Donaldson,L.W. (2006) RNA recognition by the Vts1p SAM domain. Nat. Struct. Mol. Biol., 13, 177-178.
26. Aviv,T., Amborski,A.N., Zhao,X.S., Kwan,J.J., Johnson,P.E., Sicheri,F. and Donaldson,L.W. (2006) The NMR and X-ray structures of the Saccharomyces cerevisiae Vts1 SAM domain define a surface for the recognition of RNA hairpins. J. Mol. Biol., 356, 274-279.
27. Oberstrass,F.C., Lee,A., Stefl,R., Janis,M., Chanfreau,G. and Allain,F.H. (2006) Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. Nat. Struct. Mol. Biol., 13, 160-167.
28. Aviv,T., Lin,Z., Ben-Ari,G., Smibert,C.A. and Sicheri,F. (2006) Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat. Struct. Mol. Biol., 13, 168-176.
29. Yu,X., West,S.C. and Egelman,E.H. (1997) Structure and subunit composition of the RuvAB-Holliday junction complex. J. Mol. Biol., 266, 217-222.
30. Cho,I.T., Kim,D.H., Kang,Y.H., Lee,C.H., Amangyelid,T., Nguyen,T.A., Hurwitz,J. and Seo,Y.S. (2009) Human replication factor C stimulates flap endonuclease 1. J. Biol. Chem., 284, 10387-10399.
31. Formosa,T. and Nittis,T. (1999) Dna2 mutants reveal interactions with DNA polymerase alpha and Ctf4, a Pol alpha accessory factor, and show that full Dna2 helicase activity is not essential for growth. Genetics, 151, 1459-1470.
32. Bae,K.H., Kim,H.S., Bae,S.H., Kang,H.Y., Brill,S. and Seo,Y.S. (2003) Bimodal interaction between replication-protein A and Dna2 is critical for Dna2 function both in vivo and in vitro. Nucleic Acids Res., 31, 3006-3015.
33. Kim,J.H., Kang,Y.H., Kang,H.J., Kim,D.H., Ryu,G.H., Kang,M.J. and Seo,Y.S. (2005) In vivo and in vitro studies of Mgs1 suggest a link between genome instability and Okazaki fragment processing. Nucleic Acids Res., 33, 6137-6150.