메뉴 건너뛰기




Volumn 86, Issue 5, 2012, Pages 1023-1030

Multidisciplinary perspectives on bacterial genome organization and dynamics

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN PROTEIN; DNA BINDING PROTEIN; NUCLEOID ASSOCIATED PROTEIN; UNCLASSIFIED DRUG;

EID: 84870253451     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/mmi.12055     Document Type: Conference Paper
Times cited : (7)

References (46)
  • 2
    • 0032716841 scopus 로고    scopus 로고
    • Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid
    • Ali Azam, T., 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.
    • (1999) J Bacteriol , vol.181 , pp. 6361-6370
    • Ali Azam, T.1    Iwata, A.2    Nishimura, A.3    Ueda, S.4    Ishihama, A.5
  • 3
    • 0027083350 scopus 로고
    • A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli
    • Almiron, M., Link, A.J., Furlong, D., and Kolter, R. (1992) A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev 6: 2646-2654.
    • (1992) Genes Dev , vol.6 , pp. 2646-2654
    • Almiron, M.1    Link, A.J.2    Furlong, D.3    Kolter, R.4
  • 4
    • 78649640318 scopus 로고    scopus 로고
    • Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression
    • Browning, D.F., Grainger, D.C., and Busby, S.J. (2010) Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression. Curr Opin Microbiol 13: 773-780.
    • (2010) Curr Opin Microbiol , vol.13 , pp. 773-780
    • Browning, D.F.1    Grainger, D.C.2    Busby, S.J.3
  • 5
    • 67649394401 scopus 로고    scopus 로고
    • Active transcription of rRNA operons condenses the nucleoid in Escherichia coli: examining the effect of transcription on nucleoid structure in the absence of transertion
    • Cabrera, J.E., Cagliero, C., Quan, S., Squires, C.L., and Jin, D.J. (2009) Active transcription of rRNA operons condenses the nucleoid in Escherichia coli: examining the effect of transcription on nucleoid structure in the absence of transertion. J Bacteriol 191: 4180-4185.
    • (2009) J Bacteriol , vol.191 , pp. 4180-4185
    • Cabrera, J.E.1    Cagliero, C.2    Quan, S.3    Squires, C.L.4    Jin, D.J.5
  • 6
    • 79953059399 scopus 로고    scopus 로고
    • DNA supercoiling is differentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica
    • Cameron, A.D., Stoebel, D.M., and Dorman, C.J. (2011) DNA supercoiling is differentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica. Mol Microbiol 80: 85-101.
    • (2011) Mol Microbiol , vol.80 , pp. 85-101
    • Cameron, A.D.1    Stoebel, D.M.2    Dorman, C.J.3
  • 7
    • 18444369954 scopus 로고    scopus 로고
    • The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin
    • Dame, R.T. (2005) The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol Microbiol 56: 858-870.
    • (2005) Mol Microbiol , vol.56 , pp. 858-870
    • Dame, R.T.1
  • 8
    • 0034666271 scopus 로고    scopus 로고
    • H-NS mediated compaction of DNA visualised by atomic force microscopy
    • Dame, R.T., Wyman, C., and Goosen, N. (2000) H-NS mediated compaction of DNA visualised by atomic force microscopy. Nucleic Acids Res 28: 3504-3510.
    • (2000) Nucleic Acids Res , vol.28 , pp. 3504-3510
    • Dame, R.T.1    Wyman, C.2    Goosen, N.3
  • 9
    • 33751098486 scopus 로고    scopus 로고
    • Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation
    • Dame, R.T., Noom, M.C., and Wuite, G.J. (2006) Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 444: 387-390.
    • (2006) Nature , vol.444 , pp. 387-390
    • Dame, R.T.1    Noom, M.C.2    Wuite, G.J.3
  • 10
    • 79959843457 scopus 로고    scopus 로고
    • Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria
    • Dame, R.T., Kalmykowa, O.J., and Grainger, D.C. (2011) Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria. PLoS Genet 7: e1002123.
    • (2011) PLoS Genet , vol.7
    • Dame, R.T.1    Kalmykowa, O.J.2    Grainger, D.C.3
  • 11
    • 33846465923 scopus 로고    scopus 로고
    • H-NS, the genome sentinel
    • Dorman, C.J. (2007) H-NS, the genome sentinel. Nat Rev Microbiol 5: 157-161.
    • (2007) Nat Rev Microbiol , vol.5 , pp. 157-161
    • Dorman, C.J.1
  • 12
    • 33749400168 scopus 로고    scopus 로고
    • Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements
    • Dostie, J., Richmond, T.A., Arnaout, R.A., Selzer, R.R., Lee, W.L., Honan, T.A., etal. (2006) Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16: 1299-1309.
    • (2006) Genome Res , vol.16 , pp. 1299-1309
    • Dostie, J.1    Richmond, T.A.2    Arnaout, R.A.3    Selzer, R.R.4    Lee, W.L.5    Honan, T.A.6
  • 13
    • 84870388864 scopus 로고    scopus 로고
    • Molecular basis for a protein-mediated DNA bridging mechanism that functions in long-range condensation of the E. coli chromosome
    • doi:10.1016/j.molcel.2012.09.009.
    • Dupaigne, P., Tonthat, N.K., Espeli, O., Whitfill, T., Boccard, F., and Schumacher, M.A. (2012) Molecular basis for a protein-mediated DNA bridging mechanism that functions in long-range condensation of the E. coli chromosome. Mol Cell doi:10.1016/j.molcel.2012.09.009.
    • (2012) Mol Cell
    • Dupaigne, P.1    Tonthat, N.K.2    Espeli, O.3    Whitfill, T.4    Boccard, F.5    Schumacher, M.A.6
  • 14
    • 33750495828 scopus 로고    scopus 로고
    • Organization of the Escherichia coli chromosome into macrodomains and its possible functional implications
    • Espeli, O., and Boccard, F. (2006) Organization of the Escherichia coli chromosome into macrodomains and its possible functional implications. J Struct Biol 156: 304-310.
    • (2006) J Struct Biol , vol.156 , pp. 304-310
    • Espeli, O.1    Boccard, F.2
  • 15
    • 84864147092 scopus 로고    scopus 로고
    • A MatP-divisome interaction coordinates chromosome segregation with cell division in E. coli
    • Espeli, O., Borne, R., Dupaigne, P., Thiel, A., Gigant, E., Mercier, R., and Boccard, F. (2012) A MatP-divisome interaction coordinates chromosome segregation with cell division in E. coli. EMBO J 31: 3198-3211.
    • (2012) EMBO J , vol.31 , pp. 3198-3211
    • Espeli, O.1    Borne, R.2    Dupaigne, P.3    Thiel, A.4    Gigant, E.5    Mercier, R.6    Boccard, F.7
  • 16
    • 84863117103 scopus 로고    scopus 로고
    • A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation
    • Fritsche, M., Li, S., Heermann, D.W., and Wiggins, P.A. (2012) A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation. Nucleic Acids Res 40: 972-980.
    • (2012) Nucleic Acids Res , vol.40 , pp. 972-980
    • Fritsche, M.1    Li, S.2    Heermann, D.W.3    Wiggins, P.A.4
  • 17
    • 84860381688 scopus 로고    scopus 로고
    • Higher-order chromatin structure: bridging physics and biology
    • Fudenberg, G., and Mirny, L.A. (2012) Higher-order chromatin structure: bridging physics and biology. Curr Opin Genet Dev 22: 115-124.
    • (2012) Curr Opin Genet Dev , vol.22 , pp. 115-124
    • Fudenberg, G.1    Mirny, L.A.2
  • 18
    • 79960606195 scopus 로고    scopus 로고
    • Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins
    • Gordon, B.R., Li, Y., Cote, A., Weirauch, M.T., Ding, P., Hughes, T.R., etal. (2011) Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins. Proc Natl Acad Sci USA 108: 10690-10695.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 10690-10695
    • Gordon, B.R.1    Li, Y.2    Cote, A.3    Weirauch, M.T.4    Ding, P.5    Hughes, T.R.6
  • 19
    • 44249126516 scopus 로고    scopus 로고
    • Selective repression by Fis and H-NS at the Escherichia coli dps promoter
    • Grainger, D.C., Goldberg, M.D., Lee, D.J., and Busby, S.J. (2008) Selective repression by Fis and H-NS at the Escherichia coli dps promoter. Mol Microbiol 68: 1366-1377.
    • (2008) Mol Microbiol , vol.68 , pp. 1366-1377
    • Grainger, D.C.1    Goldberg, M.D.2    Lee, D.J.3    Busby, S.J.4
  • 21
    • 33747615506 scopus 로고    scopus 로고
    • Entropy-driven spatial organization of highly confined polymers: lessons for the bacterial chromosome
    • Jun, S., and Mulder, B. (2006) Entropy-driven spatial organization of highly confined polymers: lessons for the bacterial chromosome. Proc Natl Acad Sci USA 103: 12388-12393.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 12388-12393
    • Jun, S.1    Mulder, B.2
  • 22
    • 84862917808 scopus 로고    scopus 로고
    • Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
    • Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F., and Chen, L. (2012) Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol 30: 90-98.
    • (2012) Nat Biotechnol , vol.30 , pp. 90-98
    • Kalhor, R.1    Tjong, H.2    Jayathilaka, N.3    Alber, F.4    Chen, L.5
  • 23
    • 79959670132 scopus 로고    scopus 로고
    • Super-resolution imaging of the nucleoid-associated protein HU in Caulobacter crescentus
    • Lee, S.F., Thompson, M.A., Schwartz, M.A., Shapiro, L., and Moerner, W.E. (2011) Super-resolution imaging of the nucleoid-associated protein HU in Caulobacter crescentus. Biophys J 100: L31-L33.
    • (2011) Biophys J , vol.100
    • Lee, S.F.1    Thompson, M.A.2    Schwartz, M.A.3    Shapiro, L.4    Moerner, W.E.5
  • 24
    • 33750527566 scopus 로고    scopus 로고
    • The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective
    • Luijsterburg, M.S., Noom, M.C., Wuite, G.J., and Dame, R.T. (2006) The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J Struct Biol 156: 262-272.
    • (2006) J Struct Biol , vol.156 , pp. 262-272
    • Luijsterburg, M.S.1    Noom, M.C.2    Wuite, G.J.3    Dame, R.T.4
  • 25
    • 57749209893 scopus 로고    scopus 로고
    • The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes
    • Luijsterburg, M.S., White, M.F., van Driel, R., and Dame, R.T. (2008) The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 43: 393-418.
    • (2008) Crit Rev Biochem Mol Biol , vol.43 , pp. 393-418
    • Luijsterburg, M.S.1    van White, M.F.2    Driel, R.3    Dame, R.T.4
  • 26
    • 84860512528 scopus 로고    scopus 로고
    • Evidence of non-random mutation rates suggests an evolutionary risk management strategy
    • Martincorena, I., Seshasayee, A.S., and Luscombe, N.M. (2012) Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature 485: 95-98.
    • (2012) Nature , vol.485 , pp. 95-98
    • Martincorena, I.1    Seshasayee, A.S.2    Luscombe, N.M.3
  • 28
    • 77952268971 scopus 로고    scopus 로고
    • Chromosomal periodicity and positional networks of genes in Escherichia coli
    • Mathelier, A., and Carbone, A. (2010) Chromosomal periodicity and positional networks of genes in Escherichia coli. Mol Syst Biol 6: 366.
    • (2010) Mol Syst Biol , vol.6 , pp. 366
    • Mathelier, A.1    Carbone, A.2
  • 29
    • 54949146519 scopus 로고    scopus 로고
    • The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain
    • Mercier, R., Petit, M.A., Schbath, S., Robin, S., Karoui, M.E., Boccard, F., and Espeli, O. (2008) The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain. Cell 135: 475-485.
    • (2008) Cell , vol.135 , pp. 475-485
    • Mercier, R.1    Petit, M.A.2    Schbath, S.3    Robin, S.4    Karoui, M.E.5    Boccard, F.6    Espeli, O.7
  • 30
    • 3042662444 scopus 로고    scopus 로고
    • Dps protects cells against multiple stresses during stationary phase
    • Nair, S., and Finkel, S.E. (2004) Dps protects cells against multiple stresses during stationary phase. J Bacteriol 186: 4192-4198.
    • (2004) J Bacteriol , vol.186 , pp. 4192-4198
    • Nair, S.1    Finkel, S.E.2
  • 31
    • 34250724903 scopus 로고    scopus 로고
    • Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA
    • Navarre, W.W., McClelland, M., Libby, S.J., and Fang, F.C. (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.
    • (2007) Genes Dev , vol.21 , pp. 1456-1471
    • Navarre, W.W.1    McClelland, M.2    Libby, S.J.3    Fang, F.C.4
  • 32
    • 35548978064 scopus 로고    scopus 로고
    • H-NS promotes looped domain formation in the bacterial chromosome
    • Noom, M.C., Navarre, W.W., Oshima, T., Wuite, G.J., and Dame, R.T. (2007) H-NS promotes looped domain formation in the bacterial chromosome. Curr Biol 17: R913-R914.
    • (2007) Curr Biol , vol.17
    • Noom, M.C.1    Navarre, W.W.2    Oshima, T.3    Wuite, G.J.4    Dame, R.T.5
  • 34
    • 77949570558 scopus 로고    scopus 로고
    • Mechanics of DNA bridging by bacterial condensin MukBEF in vitro and in singulo
    • Petrushenko, Z.M., Cui, Y., She, W., and Rybenkov, V.V. (2010) Mechanics of DNA bridging by bacterial condensin MukBEF in vitro and in singulo. EMBO J 29: 1126-1135.
    • (2010) EMBO J , vol.29 , pp. 1126-1135
    • Petrushenko, Z.M.1    Cui, Y.2    She, W.3    Rybenkov, V.V.4
  • 36
    • 84863969022 scopus 로고    scopus 로고
    • Galactose repressor mediated intersegmental chromosomal connections in Escherichia coli
    • Qian, Z., Dimitriadis, E.K., Edgar, R., Eswaramoorthy, P., and Adhya, S. (2012) Galactose repressor mediated intersegmental chromosomal connections in Escherichia coli. Proc Natl Acad Sci USA 109: 11336-11341.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 11336-11341
    • Qian, Z.1    Dimitriadis, E.K.2    Edgar, R.3    Eswaramoorthy, P.4    Adhya, S.5
  • 37
    • 84866147787 scopus 로고    scopus 로고
    • Rates of gyrase supercoiling and transcription elongation control supercoil density in a bacterial chromosome
    • Rovinskiy, N., Agbleke, A.A., Chesnokova, O., Pang, Z., and Higgins, N.P. (2012) Rates of gyrase supercoiling and transcription elongation control supercoil density in a bacterial chromosome. PLoS Genet 8: e1002845.
    • (2012) PLoS Genet , vol.8
    • Rovinskiy, N.1    Agbleke, A.A.2    Chesnokova, O.3    Pang, Z.4    Higgins, N.P.5
  • 38
    • 84055223488 scopus 로고    scopus 로고
    • Location and dynamics of an active promoter in Escherichia coli K-12
    • Sanchez-Romero, M.A., Lee, D.J., Sanchez-Moran, E., and Busby, S.J. (2012) Location and dynamics of an active promoter in Escherichia coli K-12. Biochem J 441: 481-485.
    • (2012) Biochem J , vol.441 , pp. 481-485
    • Sanchez-Romero, M.A.1    Lee, D.J.2    Sanchez-Moran, E.3    Busby, S.J.4
  • 39
    • 84856023505 scopus 로고    scopus 로고
    • Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle
    • Sobetzko, P., Travers, A., and Muskhelishvili, G. (2012) Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle. Proc Natl Acad Sci USA 109: E42-E50.
    • (2012) Proc Natl Acad Sci USA , vol.109
    • Sobetzko, P.1    Travers, A.2    Muskhelishvili, G.3
  • 40
    • 81255146230 scopus 로고    scopus 로고
    • The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation
    • Umbarger, M.A., Toro, E., Wright, M.A., Porreca, G.J., Bau, D., Hong, S.H., etal. (2011) The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell 44: 252-264.
    • (2011) Mol Cell , vol.44 , pp. 252-264
    • Umbarger, M.A.1    Toro, E.2    Wright, M.A.3    Porreca, G.J.4    Bau, D.5    Hong, S.H.6
  • 41
    • 84863475345 scopus 로고    scopus 로고
    • Predicting the effect of ions on the conformation of the H-NS dimerization domain
    • Vreede, J., and Dame, R.T. (2012) Predicting the effect of ions on the conformation of the H-NS dimerization domain. Biophys J 103: 89-98.
    • (2012) Biophys J , vol.103 , pp. 89-98
    • Vreede, J.1    Dame, R.T.2
  • 42
    • 80052643394 scopus 로고    scopus 로고
    • Chromosome organization by a nucleoid-associated protein in live bacteria
    • Wang, W., Li, G.W., Chen, C., Xie, X.S., and Zhuang, X. (2011) Chromosome organization by a nucleoid-associated protein in live bacteria. Science 333: 1445-1449.
    • (2011) Science , vol.333 , pp. 1445-1449
    • Wang, W.1    Li, G.W.2    Chen, C.3    Xie, X.S.4    Zhuang, X.5
  • 43
    • 77950455981 scopus 로고    scopus 로고
    • Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament
    • Wiggins, P.A., Cheveralls, K.C., Martin, J.S., Lintner, R., and Kondev, J. (2010) Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament. Proc Natl Acad Sci USA 107: 4991-4995.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 4991-4995
    • Wiggins, P.A.1    Cheveralls, K.C.2    Martin, J.S.3    Lintner, R.4    Kondev, J.5
  • 44
    • 0036050398 scopus 로고    scopus 로고
    • The role of co-transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation
    • Woldringh, C.L. (2002) The role of co-transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation. Mol Microbiol 45: 17-29.
    • (2002) Mol Microbiol , vol.45 , pp. 17-29
    • Woldringh, C.L.1
  • 45
    • 0024279845 scopus 로고
    • Transcription generates positively and negatively supercoiled domains in the template
    • Wu, H.Y., Shyy, S.H., Wang, J.C., and Liu, L.F. (1988) Transcription generates positively and negatively supercoiled domains in the template. Cell 53: 433-440.
    • (1988) Cell , vol.53 , pp. 433-440
    • Wu, H.Y.1    Shyy, S.H.2    Wang, J.C.3    Liu, L.F.4
  • 46
    • 0025003429 scopus 로고
    • An Escherichia coli protein that preferentially binds to sharply curved DNA
    • Yamada, H., Muramatsu, S., and Mizuno, T. (1990) An Escherichia coli protein that preferentially binds to sharply curved DNA. J Biochem (Tokyo) 108: 420-425.
    • (1990) J Biochem (Tokyo) , vol.108 , pp. 420-425
    • Yamada, H.1    Muramatsu, S.2    Mizuno, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.