A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions

Nucleic Acids Research

Volumn 38, Issue 11, 2010, Pages 3605-3618

  Teramoto, Jun ^a   Yoshimura, Shige H ^b   Takeyasu, Kunio ^b   Ishihama, Akira ^a  

^a HOSEI UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; ESCHERICHIA COLI PROTEIN; NUCLEOID PROTEIN; PROTEIN YGIP; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ANAEROBIC GROWTH; ARTICLE; ATOMIC FORCE MICROSCOPY; BACTERIAL CELL; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM MUTANT; BINDING SITE; DNA FOOTPRINTING; DNA MICROARRAY; DNA PROBE; DNA SEQUENCE; ESCHERICHIA COLI; GEL MOBILITY SHIFT ASSAY; GENE LOCUS; IMMUNOBLOTTING; IMMUNOFLUORESCENCE MICROSCOPY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION;

ANAEROBIOSIS; BASE SEQUENCE; BINDING SITES; DNA FOOTPRINTING; DNA, BACTERIAL; DNA-BINDING PROTEINS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENOMICS; MICROSCOPY, ATOMIC FORCE; MOLECULAR SEQUENCE DATA; SELEX APTAMER TECHNIQUE; TRANSCRIPTION FACTORS;

ESCHERICHIA COLI;

EID: 77954358334     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq077     Document Type: Article

References (46)

1. Riley,M., Abe,T., Arnaud,M.B., Berlyn,M.K., Blattner,F.R., Chaudhuri,R.R., Glasner,J.D., Horiuchi,T., Keseler,I.M., Kosuge,T. et al. (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot - 2005. Nucleic Acids Res., 34, 1-9.
2. Bachmann,B. (1996) Derivations and genotypes of some mutant derivatives of Escherichia coli K-12. In Neidhardt,F.C. et al. (eds), Escherichia coli and Salmnella. ASM Press, Washington, pp. 2460-2488.
3. Ishihama,A. (2000) Functional modulation of Escherichia coli RNA polymerase. Ann. Rev. Microbiol., 54, 499-518.
4. Perez-Rueda,E. and Collado-Vides,J. (2000) The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res., 28, 1838-1847.
5. Ishihama,A. (2009) The nucleoid: an overview. In Neidhardt,F.C. et al. (eds), Escherichia coli and Salmnella, 2nd version. ASM Press, Washington.
6. Ishihama,A. (1997) Adaptation of gene expression in stationary phase bacteria. Curr. Opn. Microbiol., 7, 582-588.
7. Shimada,T., Fujita,N., Maeda,M. and Ishihama,A. (2005) Systematic search for the Cra-binding promoters using genomic SELEX systems. Genes Cells, 10, 907-918.
8. Ogasawara,H., Hasegawa,A., Kanda,E., Miki,T., Yamamoto,K. and Ishihama,A. (2007) Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal cascade. J. Bacteriol., 187, 4791-4799.
9. Ogasawara,H., Ishida,Y., Yamada,K., Yamamoto,K. and Ishihama,A. (2007) PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli. J. Bacteriol., 189, 5534-5541.
10. Shimada,T., Hirao,K., Kori,A., Yamamoto,K. and Ishihama,A. (2007) RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. Mol. Microbiol., 66, 744-779.
11. Yang,J., Ogawa,Y., Camkaris,H., Shimada,T., Ishihama,A. and Pitard,A.J. (2007) folA, a new member of the TyrR regulon in Escherichia coli K-12. J. Bacteriol., 189, 6080-6084.
12. Umezawa,Y., Shimada,T., Kori,A., Yamada,K. and Ishihama,A. (2008) The uncharacterized transcription factor YdhM is the regulator of the nemA gene encoding N-ethylmaleimide reductase. J. Bacteriol., 190, 5890-5897.
13. Hasegawa,A., Ogasawara,H., Kori,A., Teramoto,J. and Ishihama,A. (2008) The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and utilization of purines. Microbiology, 154, 3366-3378.
14. Yamamoto,K., Matsumoto,F., Oshima,T., Fujita,N., Ogasawara,N. and Ishihama,A. (2008) Anaerobic regulation of citrate fermentation by CitAB in Escherichia coli. Biosci. Biotechnol. Biochem., 72, 3011-3014.
15. Shimada,T., Yamamoto,K. and Ishihama,A. (2009) Involvement of leucine-response transcription factor LeuO in regulation of the genes for sulfa-drug efflux. J. Bacteriol., 191, 4562-4571.
16. Ishida,U., Kori,A. and Ishihama,A. (2009) Participation of regulator AscG of the b-glucoside utilization operon in regulation of the propionate catabolism operon. J. Bacteriol, 191, 6136-6144.
17. Schell,M.A. (1993) Molecular biology of the LysR family of transcriptional regulators. Annu. Rev. Microbiol., 47, 597-626.
18. Oshima,T. and Biville,F. (2006) Functional identification of ygiP as a positive regulator of the ttdA-ttdB-ygjE operon. Microbiology, 152, 2129-2135.
19. Azam,T.A. and Ishihama,A. (1999) Twelve species of the nucleoid-associated protein from Escherichia coli: Sequence recognition specificity and DNA binding affinity. J. Biol. Chem., 274, 33105-33113.
20. Azam,T.A., Iwata,A., Nishimura,A., Ueda,S. and Ishihama,A. (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol., 181, 6361-6370.
21. Jishage,M., Iwata,A., Ueda,S. and IshIhama,A. (1996) Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions. J. Bacteriol., 178, 2507-2513.
22. Nilsson,L.A., Vanet,A., Vijgenboom,E. and Bosch,L. (1990) The role of Fis in transcription activation of stable RNA operons. EMBO J., 9, 727-737.
23. Ross,W., Thomspon,J.F., Newlands,J.T. and Gourse,G.L. (1990) E. coli Fis protein activates rRNA transcription in vitro and in vivo. EMBO J., 9, 3733-3742.
24. Almiron,M., Link,A.J., Furlog,D. and Kolter,D. (1992) A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev., 6, 2624-2654.
25. Grainger,D.C., Hurd,D., Harrison,M., Holdstock,J. and Busby,S.J.W. (2005) Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E coli chromsome. Proc. Natl Acad. Sci. USA, 102, 17693-17698.
26. Shimada,T., Makinoshima,H., Ogawa,Y., Miki,T., Maeda,T. and Ishihama,A. (2004) Classification and strength measurement of stationary-phase promoters by use of a newly developed promoter cloning vector. J. Bacteriol., 186, 7112-7122.
27. Hiraga,S., Ichinose,C., Niki,H. and Yamazoe,M. (1998) Cell cycle-dependent duplication and bidirectional migration of SeqA-associated DNA-protein complexes in E. coli. Mol. Cell, 1, 381-387.
28. Azam,T.A., Hiraga,S. and Ishihama,A. (2000) Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells, 5, 613-626.
29. Ellington,A.D. and Szostak,J.W. (1990) In vitro selection of DNA molecules that bind specific ligands. Nature, 346, 818-822.
30. Tuerk,C. and Gold,L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
31. Singer,B.S., Shtatland,T., Brown,D. and Gold,L. (1997) Libraries for genomic SELEX. Nucleic Acids Res., 25, 781-786.
32. Shimada,T., Ishihama,A., Busby,S.J. and Grainger,D.C. (2008) The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Res., 36, 3950-3955.
33. Dame,R.T., Luijsterburg,M.S., Krin,E., Berlin,P.N., Wagner,R. and Wuite,G.J. (2005) DNA bridging: a property shared among H-NS-like proteins. J. Bacteriol., 187, 1845-1848.
34. Dame,R.T., Wyman,C. and Goosen,N. (2000) H-NS mediated compaction of DNA visualized by atomic force microscopy. Nucleic Acid Res., 28, 3504-3510.
35. Kar,S., Choi,E.J., Guo,F., Dimitriadis,E.K., Kotova,S.L. and Adhya,S. (2006) Right-handed DNA supercoiling by an octmeric form of histone-like protein HU: modulation of cellular transcription. J. Biol. Chem., 281, 40144-40153.
36. Maure,S., Fritz,J., Muskhelishvili,G. and Travers,A. (2006) RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex. EMBO J., 25, 3784-3790.
37. Ceci,P., Cellai,S., Falvo,E., Rivetti,C., Rossi,G.L. and Chianocone,E. (2004) DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus. Nucleic Acid Res., 32, 5935-5944.
38. Benevides,J.M., Serban,D. and Thomas,G.J. Jr (2006) Structural perturbations induced in linear and circular DNA by the architectural protein HU from Bacillus stearothermophilus. Biochemistry, 45, 5359-5368.
39. Kim,J., Yoshimura,S.H., Hizume,K., Ohniwa,R.L., Ishihama,A. and Takeyasu,K. (2004) Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy. Nucleic Acids Res., 32, 1982-1992.
40. Ohniwa,R.L., Morikawa,K., Kim,J., Ohta,T., Ishihama,A., Wada,C. and Takeyasu,K. (2006) Dynamic state of DNA topology is essential for genome condensation in bacteria. EMBO J., 25, 5591-5602.
41. Ishihama,A. (1999) Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival. Genes Cells, 4, 135-143.
42. Chan,Y.H. and Wong,J.T. (2007) Concentration-dependent organization of DNA by the dinoflagellate histone-like protein HCc3. Nucleic Acid Res., 35, 2573-2583.
43. Ball,C.A., Osuna,R., Ferguson,K.C. and Johnson,R.C. (1992) Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J. Bacteriol., 174, 8042-8056.
44. Makinoshima,H., Nishimura,A. and Ishihama,A. (2002) Fractionation of Escherichia coli cell populations at different stages during growth transition to stationary phase. Mol. Microbiol., 43, 269-279.
45. Zheng,M., Aslund,F. and Storz,G. (1998) Activation of the OxyR transcription factor by reversible disulfide bond formation. Science, 279, 1718-1721.
46. Grainger,D.C., Hurd,D., Goldberg,M.D. and Busby,S.J.W. (2006) Association of nucleoid proteins with coding gand non-coding segments of the Escherichia coli genome. Nucleic Acids Res., 34, 4642-4652.