메뉴 건너뛰기




Volumn 178, Issue 3, 2012, Pages 260-269

Characterization of Escherichia coli nucleoids released by osmotic shock

Author keywords

Ampicillin spheroplast; DAPI UV radiation damage; Escherichia coli; Ethidium bromide; Lysozyme spheroplast; Nucleoid; Osmotic shock; Polymer physics; Protein cross links; Supercoiling

Indexed keywords

4',6 DIAMIDINO 2 PHENYLINDOLE; AMPICILLIN; BACTERIAL PROTEIN; CHLOROQUINE; DEOXYRIBONUCLEASE; DNA BINDING PROTEIN; DODECYL SULFATE SODIUM; ETHIDIUM BROMIDE; LYSOZYME; MICROSOMAL AMINOPEPTIDASE;

EID: 84861483939     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2012.03.007     Document Type: Article
Times cited : (23)

References (53)
  • 1
    • 77954376358 scopus 로고    scopus 로고
    • Direct interactions of early and late assembling division proteins in Escherichia coli cells resolved by FRET
    • Alexeeva S., Gadella T.W., Verheul J., Verhoeven G.S., den Blaauwen T. Direct interactions of early and late assembling division proteins in Escherichia coli cells resolved by FRET. Mol. Microbiol. 2010, 77:384-398.
    • (2010) Mol. Microbiol. , vol.77 , pp. 384-398
    • Alexeeva, S.1    Gadella, T.W.2    Verheul, J.3    Verhoeven, G.S.4    den Blaauwen, T.5
  • 2
    • 0023117639 scopus 로고
    • Use of site-specific recombination as a probe of DNA structure and metabolism in vivo
    • Bliska J.B., Cozzarelli N.R. Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. J. Mol. Biol. 1987, 194:205-218.
    • (1987) J. Mol. Biol. , vol.194 , pp. 205-218
    • Bliska, J.B.1    Cozzarelli, N.R.2
  • 3
    • 0022511124 scopus 로고
    • A comparison of the effect of 5-bromodeoxyuridine substitution on 33258 Hoechst- and DAPI-fluorescence of isolated chromosomes by bivariate flow karyotyping
    • Buys C.H.C.M., Mesa J., van der Veen A.Y., Aten J.A. A comparison of the effect of 5-bromodeoxyuridine substitution on 33258 Hoechst- and DAPI-fluorescence of isolated chromosomes by bivariate flow karyotyping. Histochemistry 1986, 84:462-470.
    • (1986) Histochemistry , vol.84 , pp. 462-470
    • Buys, C.H.C.M.1    Mesa, J.2    van der Veen, A.Y.3    Aten, J.A.4
  • 4
    • 0030164358 scopus 로고    scopus 로고
    • Monte Carlo simulations of randomly branched polymers with annealed and quenched branching structures
    • Cui S.M., Chen Z.Y. Monte Carlo simulations of randomly branched polymers with annealed and quenched branching structures. Phys. Rev. E 1996, 53:6238-6243.
    • (1996) Phys. Rev. E , vol.53 , pp. 6238-6243
    • Cui, S.M.1    Chen, Z.Y.2
  • 6
    • 0035782861 scopus 로고    scopus 로고
    • Polymer-mediated compaction and internal dynamics of isolated Escherichia coli nucleoids
    • Cunha S., Woldringh C.L., Odijk T. Polymer-mediated compaction and internal dynamics of isolated Escherichia coli nucleoids. J. Struct. Biol. 2001, 136:53-66.
    • (2001) J. Struct. Biol. , vol.136 , pp. 53-66
    • Cunha, S.1    Woldringh, C.L.2    Odijk, T.3
  • 7
    • 18144393456 scopus 로고    scopus 로고
    • Restricted diffusion of DNA segments within the isolated Escherichia coli nucleoid
    • Cunha S., Woldringh C.L., Odijk T. Restricted diffusion of DNA segments within the isolated Escherichia coli nucleoid. J. Struct. Biol. 2005, 150:226-232.
    • (2005) J. Struct. Biol. , vol.150 , pp. 226-232
    • Cunha, S.1    Woldringh, C.L.2    Odijk, T.3
  • 8
    • 0019624075 scopus 로고
    • Conformation of branched polymers
    • Daoud M., Joanny J.F. Conformation of branched polymers. J. Physique 1981, 42:1359-1371.
    • (1981) J. Physique , vol.42 , pp. 1359-1371
    • Daoud, M.1    Joanny, J.F.2
  • 9
    • 0016384737 scopus 로고
    • Electron microscopic visualization of the folded chromosome of Escherichia coli
    • Delius H., Worcel A. Electron microscopic visualization of the folded chromosome of Escherichia coli. J. Mol. Biol. 1974, 82:107-109.
    • (1974) J. Mol. Biol. , vol.82 , pp. 107-109
    • Delius, H.1    Worcel, A.2
  • 10
    • 0016774266 scopus 로고
    • Conformational transitions in the Escherichia coli chromosome: analysis by viscometry and sedimentation
    • Drlica K., Worcel A. Conformational transitions in the Escherichia coli chromosome: analysis by viscometry and sedimentation. J. Mol. Biol. 1975, 98:393-411.
    • (1975) J. Mol. Biol. , vol.98 , pp. 393-411
    • Drlica, K.1    Worcel, A.2
  • 11
    • 0017889516 scopus 로고
    • Association of the folded chromosome with the cell envelope of Escherichia coli: nature of the membrane-associated DNA
    • Drlica K., Burgi E., Worcel A. Association of the folded chromosome with the cell envelope of Escherichia coli: nature of the membrane-associated DNA. J. Bacteriol. 1978, 134:1108-1116.
    • (1978) J. Bacteriol. , vol.134 , pp. 1108-1116
    • Drlica, K.1    Burgi, E.2    Worcel, A.3
  • 12
    • 77951920988 scopus 로고    scopus 로고
    • Macromolecular crowding can acoount for RNase-sensitive constraint of bacterial nucleoid structure
    • Foley P.L., Wilson D.B., Shuler M.L. Macromolecular crowding can acoount for RNase-sensitive constraint of bacterial nucleoid structure. Biochem. Biophys. Res. Comm. 2010, 395:42-47.
    • (2010) Biochem. Biophys. Res. Comm. , vol.395 , pp. 42-47
    • Foley, P.L.1    Wilson, D.B.2    Shuler, M.L.3
  • 13
    • 0019074080 scopus 로고
    • Simple purification and properties of bovine pancreatic deoxyribonuclease I
    • Funakoshi A., Tsubota Y., Fujii K., Ibayashi H., Takagi Y. Simple purification and properties of bovine pancreatic deoxyribonuclease I. J. Biochem. 1980, 88:1113-1118.
    • (1980) J. Biochem. , vol.88 , pp. 1113-1118
    • Funakoshi, A.1    Tsubota, Y.2    Fujii, K.3    Ibayashi, H.4    Takagi, Y.5
  • 14
    • 0016610022 scopus 로고
    • Size and DNA content of purified E. coli nucleoids observed by fluorescence microscopy
    • Hecht R.M., Taggart R.T., Pettijohn D.E. Size and DNA content of purified E. coli nucleoids observed by fluorescence microscopy. Nature 1975, 253:60-62.
    • (1975) Nature , vol.253 , pp. 60-62
    • Hecht, R.M.1    Taggart, R.T.2    Pettijohn, D.E.3
  • 15
    • 0017328197 scopus 로고
    • Sedimentation properties of the bacterial chromosome as an isolated nucleoid and as an unfolded DNA fiber
    • Hecht R.M., Stimpson D., Pettijohm D. Sedimentation properties of the bacterial chromosome as an isolated nucleoid and as an unfolded DNA fiber. J. Mol. Biol. 1977, 111:257-277.
    • (1977) J. Mol. Biol. , vol.111 , pp. 257-277
    • Hecht, R.M.1    Stimpson, D.2    Pettijohm, D.3
  • 16
    • 0029863159 scopus 로고    scopus 로고
    • Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium
    • Higgins N.P., Yang X., Fu Q., Roth J.R. Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium. J. Bacteriol. 1996, 178:2825-2835.
    • (1996) J. Bacteriol. , vol.178 , pp. 2825-2835
    • Higgins, N.P.1    Yang, X.2    Fu, Q.3    Roth, J.R.4
  • 17
    • 0014632465 scopus 로고
    • The amino acid nature of ampicillin and related penicillins
    • Hout J.P., Poole J.W. The amino acid nature of ampicillin and related penicillins. J. Pharma. Sci. 1969, 58:1510-1515.
    • (1969) J. Pharma. Sci. , vol.58 , pp. 1510-1515
    • Hout, J.P.1    Poole, J.W.2
  • 19
    • 0018404456 scopus 로고
    • Comparative viscometric analysis of the interaction of chloroquine and quinacrine with superhelical and sonicated DNA
    • Jones R.L., Davidson M.W., Wilson W.D. Comparative viscometric analysis of the interaction of chloroquine and quinacrine with superhelical and sonicated DNA. Biochim. Biophys. Acta 1979, 561:77-84.
    • (1979) Biochim. Biophys. Acta , vol.561 , pp. 77-84
    • Jones, R.L.1    Davidson, M.W.2    Wilson, W.D.3
  • 20
    • 0028289997 scopus 로고
    • Photodegradation studies on chloroquine phosphate by high-performance liquid chromatography
    • Karim E.I., Ibrahim K.E., Abdelrahman A.N., Fell A.F. Photodegradation studies on chloroquine phosphate by high-performance liquid chromatography. J. Pharm. Biomed. Anal. 1994, 12:667-674.
    • (1994) J. Pharm. Biomed. Anal. , vol.12 , pp. 667-674
    • Karim, E.I.1    Ibrahim, K.E.2    Abdelrahman, A.N.3    Fell, A.F.4
  • 21
    • 0017045430 scopus 로고
    • Electron microscopy of membrane-free folded chromosomes from Escherichia coli
    • Kavenoff R., Bowen B.C. Electron microscopy of membrane-free folded chromosomes from Escherichia coli. Chromosoma 1976, 59:89-101.
    • (1976) Chromosoma , vol.59 , pp. 89-101
    • Kavenoff, R.1    Bowen, B.C.2
  • 22
    • 0343992911 scopus 로고
    • Replication of the Escherichia coli chromosome with a soluble enzyme system
    • Kornberg T., Lockwood A., Worcel A. Replication of the Escherichia coli chromosome with a soluble enzyme system. Proc. Natl. Acad. Sci. USA 1974, 71:3189-3193.
    • (1974) Proc. Natl. Acad. Sci. USA , vol.71 , pp. 3189-3193
    • Kornberg, T.1    Lockwood, A.2    Worcel, A.3
  • 23
    • 0001742688 scopus 로고    scopus 로고
    • Lysozyme net charge and ion binding in concentrated aqueous electrolyte solutions
    • Kuehner D.E., Engmann J., Fergg F., Wernick M., Blanch H.W., et al. Lysozyme net charge and ion binding in concentrated aqueous electrolyte solutions. J. Phys. Chem. B 1999, 103:1368-1374.
    • (1999) J. Phys. Chem. B , vol.103 , pp. 1368-1374
    • Kuehner, D.E.1    Engmann, J.2    Fergg, F.3    Wernick, M.4    Blanch, H.W.5
  • 25
    • 0028000456 scopus 로고
    • Fluctuations and supercoiling of DNA
    • Marko J.F., Siggia E.D. Fluctuations and supercoiling of DNA. Science 1994, 265:506-508.
    • (1994) Science , vol.265 , pp. 506-508
    • Marko, J.F.1    Siggia, E.D.2
  • 26
    • 0017845034 scopus 로고
    • Nucleoid release from Escherichia coli cells
    • Materman E.C., van Gool A.P. Nucleoid release from Escherichia coli cells. J. Bacteriol. 1978, 133:878-883.
    • (1978) J. Bacteriol. , vol.133 , pp. 878-883
    • Materman, E.C.1    van Gool, A.P.2
  • 27
    • 0017274282 scopus 로고
    • Factors affecting the release of folded chromosomes from Escherichia coli
    • Meijer M., de Jong M.A., Woldringh C.L., Nanninga N. Factors affecting the release of folded chromosomes from Escherichia coli. Eur. J. Biochem. 1976, 63:469-475.
    • (1976) Eur. J. Biochem. , vol.63 , pp. 469-475
    • Meijer, M.1    de Jong, M.A.2    Woldringh, C.L.3    Nanninga, N.4
  • 29
    • 0034513957 scopus 로고    scopus 로고
    • Multiple restraints to the unfolding of spermidine nucleoids from Escherichia coli
    • Murphy L.D., Zimmerman S.B. Multiple restraints to the unfolding of spermidine nucleoids from Escherichia coli. J. Struct. Biol. 2000, 132:46-62.
    • (2000) J. Struct. Biol. , vol.132 , pp. 46-62
    • Murphy, L.D.1    Zimmerman, S.B.2
  • 31
    • 0032514107 scopus 로고    scopus 로고
    • Osmotic compaction of supercoiled DNA into a bacterial nucleoid
    • Odijk T. Osmotic compaction of supercoiled DNA into a bacterial nucleoid. Biophys. Chem. 1998, 73:23-30.
    • (1998) Biophys. Chem. , vol.73 , pp. 23-30
    • Odijk, T.1
  • 32
    • 0033879014 scopus 로고    scopus 로고
    • Dynamics of the expanding DNA nucleoid released from a bacterial cell
    • Odijk T. Dynamics of the expanding DNA nucleoid released from a bacterial cell. Physica A 2000, 277:62-70.
    • (2000) Physica A , vol.277 , pp. 62-70
    • Odijk, T.1
  • 33
    • 0036876813 scopus 로고    scopus 로고
    • Sedimentation of DNA supercoils and bacterial nucleoids
    • Odijk T. Sedimentation of DNA supercoils and bacterial nucleoids. Colloids and Surf. A: Physicochem. Eng. Aspects 2002, 210:191-197.
    • (2002) Colloids and Surf. A: Physicochem. Eng. Aspects , vol.210 , pp. 191-197
    • Odijk, T.1
  • 34
    • 0027524617 scopus 로고
    • Chromosomal domains of supercoiling in Salmonella typhimurium
    • Pavitt G.D., Higgins C.F. Chromosomal domains of supercoiling in Salmonella typhimurium. Mol. Microbiol. 1993, 10:685-696.
    • (1993) Mol. Microbiol. , vol.10 , pp. 685-696
    • Pavitt, G.D.1    Higgins, C.F.2
  • 35
    • 0015708687 scopus 로고
    • RNA molecules bound to the folded bacterial genome stabilize DNA folds and segregate domains of supercoiling
    • Pettijohn D.E., Hecht R. RNA molecules bound to the folded bacterial genome stabilize DNA folds and segregate domains of supercoiling. Cold Spring Harbor Symp. Quant. Biol. 1973, 38:31-42.
    • (1973) Cold Spring Harbor Symp. Quant. Biol. , vol.38 , pp. 31-42
    • Pettijohn, D.E.1    Hecht, R.2
  • 36
    • 0020445968 scopus 로고
    • Structure and properties of the bacterial nucleoid
    • Pettijohn D.E. Structure and properties of the bacterial nucleoid. Cell 1982, 30:667-669.
    • (1982) Cell , vol.30 , pp. 667-669
    • Pettijohn, D.E.1
  • 37
    • 0000663451 scopus 로고
    • Structure of the isolated nucleoid
    • Academic Press, London, New York, N. Nanninga (Ed.)
    • Pettijohn D.E., Sinden R.R. Structure of the isolated nucleoid. Molecular Cytology of Escherichia coli 1985, 199-227. Academic Press, London, New York. N. Nanninga (Ed.).
    • (1985) Molecular Cytology of Escherichia coli , pp. 199-227
    • Pettijohn, D.E.1    Sinden, R.R.2
  • 38
    • 0022181017 scopus 로고
    • DNA topoisomeras I mutants. Increased heterogeneity in linking number and other replicon-dependent changes in DNA supercoiling
    • Pruss G.J. DNA topoisomeras I mutants. Increased heterogeneity in linking number and other replicon-dependent changes in DNA supercoiling. J. Mol. Biol. 1985, 185:51-63.
    • (1985) J. Mol. Biol. , vol.185 , pp. 51-63
    • Pruss, G.J.1
  • 39
  • 40
    • 34147130136 scopus 로고    scopus 로고
    • Internal structure and dynamics of isolated Escherichia coli nucleoids assessed by fluorescence correlation spectroscopy
    • Romantsov T., Fishov I., Krichevsky O. Internal structure and dynamics of isolated Escherichia coli nucleoids assessed by fluorescence correlation spectroscopy. Biophys. J. 2007, 92:2875-2884.
    • (2007) Biophys. J. , vol.92 , pp. 2875-2884
    • Romantsov, T.1    Fishov, I.2    Krichevsky, O.3
  • 41
    • 0343240577 scopus 로고
    • Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling
    • Sinden R.R., Pettijohn D.E. Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling. Proc. Natl. Acad. Sci. USA 1981, 78:224-228.
    • (1981) Proc. Natl. Acad. Sci. USA , vol.78 , pp. 224-228
    • Sinden, R.R.1    Pettijohn, D.E.2
  • 42
    • 0020687475 scopus 로고
    • Folding of prokaryotic DNA: isolation and characterization of nucleoids from Bacillus licheniformis
    • Sloof P., Maagdelijn A., Boswinkel E. Folding of prokaryotic DNA: isolation and characterization of nucleoids from Bacillus licheniformis. J. Mol. Biol. 1983, 163:277-297.
    • (1983) J. Mol. Biol. , vol.163 , pp. 277-297
    • Sloof, P.1    Maagdelijn, A.2    Boswinkel, E.3
  • 43
    • 0014984183 scopus 로고
    • The folded genome of Escherichia coli isolated in a protein-DNA-RNA complex
    • Stonington G.O., Pettijohn D.E. The folded genome of Escherichia coli isolated in a protein-DNA-RNA complex. Proc. Natl. Acad. Sci. USA 1971, 68:6-9.
    • (1971) Proc. Natl. Acad. Sci. USA , vol.68 , pp. 6-9
    • Stonington, G.O.1    Pettijohn, D.E.2
  • 44
    • 0345455600 scopus 로고
    • Hydrogen ion equilibria of ribonuclease
    • Tanford Ch., Hauenstein J.D. Hydrogen ion equilibria of ribonuclease. J. Amer. Chem. Soc. 1956, 78:5287-5291.
    • (1956) J. Amer. Chem. Soc. , vol.78 , pp. 5287-5291
    • Tanford, C.1    Hauenstein, J.D.2
  • 46
    • 0033062960 scopus 로고    scopus 로고
    • Electrostatic-undulatory theory of plectonemically supercoiled DNA
    • Ubbink J., Odijk Th. Electrostatic-undulatory theory of plectonemically supercoiled DNA. Biophys. J. 1999, 76:2502-2519.
    • (1999) Biophys. J. , vol.76 , pp. 2502-2519
    • Ubbink, J.1    Odijk, T.2
  • 47
    • 49049146776 scopus 로고
    • The osmotic pressure of concentrated protein solutions: effect of concentration and pH in saline solutions of bovine serum albumin
    • Vilker V.L., Colton C.K., Smith K.A. The osmotic pressure of concentrated protein solutions: effect of concentration and pH in saline solutions of bovine serum albumin. J. Coll. Int. Sci. 1981, 79:548-566.
    • (1981) J. Coll. Int. Sci. , vol.79 , pp. 548-566
    • Vilker, V.L.1    Colton, C.K.2    Smith, K.A.3
  • 48
    • 0030058275 scopus 로고    scopus 로고
    • Effect of supercoiling on the juxtaposition and relative orientation of DNA sites
    • Vologodskii A., Cozzarelli N.R. Effect of supercoiling on the juxtaposition and relative orientation of DNA sites. Biophys. J. 1996, 70:2548-2556.
    • (1996) Biophys. J. , vol.70 , pp. 2548-2556
    • Vologodskii, A.1    Cozzarelli, N.R.2
  • 49
    • 0001115291 scopus 로고
    • Structure of nucleoid and cytoplasm in the intact cell
    • Academic Press, London, New York, N. Nanninga (Ed.)
    • Woldringh C.L., Nanninga N. Structure of nucleoid and cytoplasm in the intact cell. "Molecular cytology of Escherichia coli" 1985, 161-197. Academic Press, London, New York. N. Nanninga (Ed.).
    • (1985) "Molecular cytology of Escherichia coli" , pp. 161-197
    • Woldringh, C.L.1    Nanninga, N.2
  • 50
    • 0015506478 scopus 로고
    • On the structure of the folded chromosome of E. coli
    • Worcel A., Burgi E. On the structure of the folded chromosome of E. coli. J. Mol. Biol. 1972, 71:127-147.
    • (1972) J. Mol. Biol. , vol.71 , pp. 127-147
    • Worcel, A.1    Burgi, E.2
  • 51
    • 0015950236 scopus 로고
    • Properties of a membrane-attached form of the folded chromosome of Escherichia coli
    • Worcel A., Burgi E. Properties of a membrane-attached form of the folded chromosome of Escherichia coli. J. Mol. Biol. 1974, 82:91-105.
    • (1974) J. Mol. Biol. , vol.82 , pp. 91-105
    • Worcel, A.1    Burgi, E.2
  • 52
    • 31344453142 scopus 로고    scopus 로고
    • Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase
    • Zimmerman S.B. Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase. J. Struct. Biol. 2006, 153:160-175.
    • (2006) J. Struct. Biol. , vol.153 , pp. 160-175
    • Zimmerman, S.B.1
  • 53
    • 33750510057 scopus 로고    scopus 로고
    • Shape and compaction of Escherichia coli nucleoids
    • Zimmerman S.B. Shape and compaction of Escherichia coli nucleoids. J. Struct. Biol. 2006, 156:255-261.
    • (2006) J. Struct. Biol. , vol.156 , pp. 255-261
    • Zimmerman, S.B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.