Gene 5.5 protein of bacteriophage T7 in complex with Escherichia coli nucleoid protein H-NS and transfer RNA masks transfer RNA priming in T7 DNA replication

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 21, 2012, Pages 8050-8055

  Zhu, Bin ^a   Lee, Seung Joo ^a   Tan, Min ^b   Wang, En Duo ^b   Richardson, Charles C ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b Chinese Academy of Sciences   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DNA PRIMASE; ENDONUCLEASE; GENE 5.5 PROTEIN; PRIMER RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; BACTERIOPHAGE T7; DNA REPLICATION; ENZYME ACTIVITY; ESCHERICHIA COLI; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA TRANSPORT;

BACTERIOPHAGE T7; DNA HELICASES; DNA PRIMASE; DNA PRIMERS; DNA REPLICATION; ENDONUCLEASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FIMBRIAE PROTEINS; GENE EXPRESSION REGULATION, VIRAL; PLASMIDS; RNA, TRANSFER; VIRAL PROTEINS;

ESCHERICHIA COLI;

EID: 84861445862     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1205990109     Document Type: Article

References (31)

1. Frick DN, Richardson CC (2001) DNA primases. Annu Rev Biochem 70:39-80. (Pubitemid 32662205)
2. Yuzhakov A, Kelman Z, O'Donnell M (1999) Trading places on DNA - a three-point switch underlies primer handoff from primase to the replicative DNA polymerase. Cell 96:153-163.
3. Zhu B, Lee SJ, Richardson CC (2010) Direct role for the RNA polymerase domain of T7 primase in primer delivery. Proc Natl Acad Sci USA 107:9099-9104.
4. Hamdan SM, Richardson CC (2009) Motors, switches, and contacts in the replisome. Annu Rev Biochem 78:205-243.
5. Dunn JJ, Studier FW (1983) Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J Mol Biol 166:477-535. (Pubitemid 13027896)
6. Lee SJ, Zhu B, Hamdan SM, Richardson CC (2010) Mechanism of sequence-specific template binding by the DNA primase of bacteriophage T7. Nucleic Acids Res 38:4372-4383.
7. Akabayov B, et al. (2009) DNA recognition by the DNA primase of bacteriophage T7: A structure-function study of the zinc-binding domain. Biochemistry 48:1763-1773.
8. Mendelman LV, Notarnicola SM, Richardson CC (1992) Roles of bacteriophage T7 gene 4 proteins in providing primase and helicase functions in vivo. Proc Natl Acad Sci USA 89:10638-10642.
9. Lee SJ, Richardson CC (2005) Acidic residues in the nucleotide-binding site of the bacteriophage T7 DNA primase. J Biol Chem 280:26984-26991.
10. Liu Q, Richardson CC (1993) Gene 5.5 protein of bacteriophage T7 inhibits the nucleoid protein H-NS of Escherichia coli. Proc Natl Acad Sci USA 90:1761-1765. (Pubitemid 23069936)
11. Ali SS, Beckett E, Bae SJ, NavarreWW(2011) The 5.5 protein of phage T7 inhibits H-NS through interactions with the central oligomerization domain. J Bacteriol 193:4881-4892.
12. Ibba M, Söll D (2000) Aminoacyl-tRNA synthesis. Annu Rev Biochem 69:617-650.
13. Dorman CJ (2007) H-NS, the genome sentinel. Nat Rev Microbiol 5:157-161.
14. Navarre WW, McClelland M, Libby SJ, Fang FC (2007) Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA. Genes Dev 21:1456-1471. (Pubitemid 46955718)
15. Dong H, Nilsson L, Kurland CG (1996) Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol 260:649-663. (Pubitemid 26270960)
16. Zhu B, Lee SJ, Richardson CC (2011) Bypass of a nick by the replisome of bacteriophage T7. J Biol Chem 286:28488-28497.
17. Center MS, Studier FW, Richardson CC (1970) The structural gene for a T7 endonuclease essential for phage DNA synthesis. Proc Natl Acad Sci USA 65:242-248.
18. Hadden JM, Déclais AC, Carr SB, Lilley DM, Phillips SE (2007) The structural basis of Holliday junction resolution by T7 endonuclease I. Nature 449:621-624. (Pubitemid 47525149)
19. Brescia CC, Kaw MK, Sledjeski DD (2004) The DNA binding protein H-NS binds to and alters the stability of RNA in vitro and in vivo. J Mol Biol 339:505-514. (Pubitemid 38625903)
20. Tisné C (2005) Structural bases of the annealing of primer tRNA(3Lys) to the HIV-1 viral RNA. Curr HIV Res 3:147-156.
21. Hamdan SM, Loparo JJ, Takahashi M, Richardson CC, van Oijen AM (2009) Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis. Nature 457:336-339.
22. López de Saro FJ, Georgescu RE, O'Donnell M (2003) A peptide switch regulates DNA polymerase processivity. Proc Natl Acad Sci USA 100:14689-14694. (Pubitemid 37517952)
23. Serwer P, Watson RH, Son M (1990) Role of gene 6 exonuclease in the replication and packaging of bacteriophage T7 DNA. J Mol Biol 215:287-299. (Pubitemid 20329750)
24. Sharadamma N, Harshavardhana Y, Singh P, Muniyappa K (2010) Mycobacterium tuberculosis nucleoid-associated DNA-binding protein H-NS binds with high-affinity to the Holliday junction and inhibits strand exchange promoted by RecA protein. Nucleic Acids Res 38:3555-3569.
25. Friedrich K, Gualerzi CO, Lammi M, Losso MA, Pon CL (1988) Proteins from the prokaryotic nucleoid. Interaction of nucleic acids with the 15 kDa Escherichia coli histone-like protein H-NS. FEBS Lett 229:197-202.
26. Moore SD, Sauer RT (2007) The tmRNA system for translational surveillance and ribosome rescue. Annu Rev Biochem 76:101-124.
27. Lee SJ, Chowdhury K, Tabor S, Richardson CC (2009) Rescue of bacteriophage T7 DNA polymerase of low processivity by suppressor mutations affecting gene 3 endonuclease. J Virol 83:8418-8427.
28. Bernstein JA, Richardson CC (1988) Purification of the 56-kDa component of the bacteriophage T7 primase/helicase and characterization of its nucleoside 5′-triphosphatase activity. J Biol Chem 263:14891-14899.
29. Tabor S, Huber HE, Richardson CC (1987) Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7. J Biol Chem 262:16212-16223.
30. (Leu). Sci China C Life Sci 41:225-231.
31. Tan M, et al. (2010) tRNA-dependent pre-transfer editing by prokaryotic leucyl-tRNA synthetase. J Biol Chem 285:3235-3244.