Mutations in the essential escherichia coli gene, yqgF, and their effects on transcription

Journal of Molecular Microbiology and Biotechnology

Volumn 22, Issue 1, 2012, Pages 17-23

  Iwamoto, Akira ^a   Osawa, Atsushi ^a   Kawai, Makiko ^a   Honda, Hirofumi ^a   Yoshida, Saori ^a   Furuya, Nobuhisa ^a   Kato, Jun Ichi ^a  

^a TOKYO METROPOLITAN UNIVERSITY   (Japan)

Author keywords

Escherichia coli; Essential genes; NusA; Rho; Transcription termination

Indexed keywords

BACTERIAL PROTEIN; BETA GALACTOSIDASE; BICOZAMYCIN; RHO FACTOR;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; CONTROLLED STUDY; ESCHERICHIA COLI; GENE IDENTIFICATION; GENE ISOLATION; GENE MUTATION; GENE STRUCTURE; GENETIC TRANSCRIPTION; NONHUMAN; PLASMID; REAL TIME POLYMERASE CHAIN REACTION; YQGF GENE;

ENDODEOXYRIBONUCLEASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENES, ESSENTIAL; MUTANT PROTEINS; MUTATION; RHO FACTOR; TERMINATOR REGIONS, GENETIC; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 84857135683     PISSN: 14641801     EISSN: 16602412     Source Type: Journal    
DOI: 10.1159/000336517     Document Type: Article

References (42)

1. Adhya S, Gottesman M: Control of transcription termination. Annu Rev Biochem 1978; 47: 967-996.
2. Adkins MW, Tyler JK: Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions. Mol Cell 2006; 21: 405-416. (Pubitemid 43163535)
3. Aravind L, Makarova KS, Koonin EV: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res 2000; 28: 3417-3432.
4. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H: Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006; 2: 2006.0008.
5. Bar-Nahum G, Epshtein V, Ruckenstein AE, Rafikov R, Mustaev A, Nudler E: A ratchet mechanism of transcription elongation and its control. Cell 2005; 120: 183-193. (Pubitemid 40174762)
6. Burmann BM, Schweimer K, Luo X, Wahl MC, Stitt BL, Gottesman ME, Rösch P: A NusE: NusG complex links transcription and translation. Science 2010; 328: 501-504.
7. Burns CM, Nowatzke WL, Richardson JP: Activation of Rho-dependent transcription termination by NusG. Dependence on terminator location and acceleration of RNA release. J Biol Chem 1999; 274: 5245-5251.
8. Cardinale CJ, Washburn RS, Tadigotla VR, Brown LM, Gottesman ME, Nudler E: Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli . Science 2008; 320: 935-938. (Pubitemid 351929589)
9. Ciampi MS: Rho-dependent terminators and transcription termination. Microbiology 2006; 152: 2515-2528. (Pubitemid 44405077)
10. Cohen SE, Godoy VG, Walker GC: Transcriptional modulator NusA interacts with translesion DNA polymerases in Escherichia coli . J Bacteriol 2009; 191: 665-672.
11. Cohen SE, Lewis CA, Mooney RA, Kohanski MA, Collins JJ, Landick R, Walker GC: Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli . Proc Natl Acad Sci USA 2010; 107: 15517-15522.
12. Condon C, Squires C, Squires CL: Control of rRNA transcription in Escherichia coli . Microbiol Rev 1995; 59: 623-645.
13. Court D, Brady C, Rosenberg M, Wulff DL, Behr M, Mahoney M, Izumi SU: Control of transcription termination: a rho-dependent termination site in bacteriophage lambda. J Mol Biol 1980; 138: 231-254. (Pubitemid 10044380)
14. De Crombrugghe B, Adhya S, Gottesman M, Pastan I: Effect of Rho on transcription of bacterial operons. Nat New Biol 1973; 241: 260-264.
15. Epshtein V, Dutta D, Wade J, Nudler E: An allosteric mechanism of Rho-dependent transcription termination. Nature 2010; 463: 245-249.
16. Freiberg C, Wieland B, Spaltmann F, Ehlert K, Brötz H, Labischinski H: Identification of novel essential Escherichia coli genes conserved among pathogenic bacteria. J Mol Microbiol Biotechnol 2001; 3: 483-489. (Pubitemid 32421672)
17. Friedman DI, Court DL: Transcription antitermination: the lambda paradigm updated. Mol Microbiol 1995; 18: 191-200.
18. Hashimoto-Gotoh T, Franklin FC, Nordheim A, Timmis KN: Specific-purpose plasmid cloning vectors. I. Low copy number, temperature-sensitive, mobilization-defective pSC101-derived containment vectors. Gene 1981; 16: 227-235. (Pubitemid 12132053)
19. He X, Thornton J, Carmicle-Davis S, McDaniel LS: Tex, a putative transcriptional accessory factor, is involved in pathogen fitness in accessory factor, is involved in pathogen fitness in Streptococcus pneumoniae . Microb Pathog 2006; 41: 199-206. (Pubitemid 44636117)
20. Hidalgo AA, Trombert AN, Castro-Alonso JC, Santiviago CA, Tesser BR, Youderian P, Mora GC: Insertions of mini-Tn10 transposon T-POP in Salmonella enterica sv. typhi . Genetics 2004; 167: 1069-1077. (Pubitemid 39045618)
21. Iwamoto A, Lemire S, Yonesaki T: Post-transcriptional control of Crp-cAMP by RNase LS in Escherichia coli . Mol Microbiol 2008; 70: 1570-1578.
22. Johnson SJ, Close D, Robinson H, Vallet-Gely I, Dove SL, Hill CP: Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa . J Mol Biol 2008; 377: 1460-1473.
23. Kalyani BS, Muteeb G, Qayyum MZ, Sen R: Interaction with the nascent RNA is a prerequisite for the recruitment of Rho to the transcription elongation complex in vitro. J Mol Biol 2011; 413: 548-560.
24. Kato J, Ikeda H: Construction of mini-F plasmid vectors for plasmid shuffling in Escherichia coli . Gene 1996; 170: 141-142. (Pubitemid 26130809)
25. Kato J, Hashimoto M: Construction of consecutive deletions of the Escherichia coli chromosome. Mol Syst Biol 2007; 3: 132.
26. Kato J, Hashimoto M: Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome; in Osterman AL, Gerdes SY (eds): Microbial Gene Essentiality, Protocols and Bioinformatics: Methods in Molecular Biology. Totowa, Humana Press, 2008, pp 279-299.
27. Konan K, Yanofsky C: Rho-dependent transcription termination in the tna operon of Escherichia coli : roles of the boxA sequence and the rut site. J Bacteriol 2000; 182: 3981-3988. (Pubitemid 30436559)
28. Lee HJ, Jeon HJ, Ji SC, Yun SH, Lim HM: Establishment of an mRNA gradient depends on the promoter: an investigation of polarity in gene expression. J Mol Biol 2008; 378: 318-327.
29. Liu D, Wang YS, Wyss DF: Solution structure of the hypothetical protein YqgF from Escherichia coli reveals an RNAse H fold. J Biomol NMR 2003; 27: 389-392. (Pubitemid 37322110)
30. McGlynn P: Linking transcription with DNA repair, damage tolerance, and genome duplication. Proc Natl Acad Sci USA 2010; 107: 15314-15315.
31. Mooney RA, Davis SE, Peters JM, Rowland JL, Ansari AZ, Landick R: Regulator trafficking on bacterial transcription units in vivo. Mol Cell 2009; 33: 97-108.
32. Peters JM, Mooney RA, Kuan PF, Rowland JL, Keles S, Landick R: Rho directs widespread termination of intragenic and stable RNA transcription. Proc Natl Acad Sci USA 2009; 106: 15406-15411.
33. Peters JM, Vangeloff AD, Landick R: Bacterial transcription terminators: the RNA 3'-end chronicles. J Mol Biol 2011; 412: 793-813.
34. Platt T, Bear DG: Role of RNA polymerase,-factor, and ribosomes in transcription termination; in Beckwith J, Davies J, Gallant JA (eds): Gene Function in Prokaryotes. Cold Spring Harbor, Cold Spring Harbor Laboratory Press, 1983, pp 123-161.
35. Ponting CP: Novel domains and orthologues of eukaryotic transcription elongation factors. Nucleic Acids Res 2002; 30: 3643-3652. (Pubitemid 35021228)
36. Proshkin S, Rahmouni AR, Mironov A, Nudler E: Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 2010; 328: 504-508.
37. Roberts JW: Syntheses that stay together. Science 2010; 328: 436-437.
38. Ruteshouser EC, Richardson JP: Identification and characterization of transcription termination sites in the Escherichia coli lacZ gene. J Mol Biol 1989; 208: 23-43. (Pubitemid 19191514)
39. Saito A, Iwasaki H, Ariyoshi M, Morikawa K, Shinagawa H: Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase. Proc Natl Acad Sci USA 1995; 92: 7470-7474.
40. Svetlov V, Belogurov GA, Shabrova E, Vassylyev DG, Artsimovitch I: Allosteric control of the RNA polymerase by the elongation factor RfaH. Nucleic Acids Res 2007; 35: 5694-5705. (Pubitemid 47506287)
41. Washburn RS, Gottesman ME: Transcription termination maintains chromosome integrity. Proc Natl Acad Sci USA 2011; 108: 792-797.
42. Zhang X, Bremer H: Control of the Escherichia coli rrnB P1 promoter strength by ppGpp. J Biol Chem 1995; 270: 11181-11189.