메뉴 건너뛰기




Volumn 37, Issue 5, 2009, Pages 1463-1476

Insights into the architecture and stoichiometry of Escherichia coli PepA·DNA complexes involved in transcriptional control and site-specific DNA recombination by atomic force microscopy

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CARBAMATE KINASE; DEOXYRIBONUCLEOPROTEIN; ESCHERICHIA COLI PROTEIN; GLUTAMYL AMINOPEPTIDASE; INTEGRATION HOST FACTOR; PURINE; PYRIMIDINE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR PURR; TRANSCRIPTION FACTOR RUTR; UNCLASSIFIED DRUG;

EID: 63249100571     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn1078     Document Type: Article
Times cited : (32)

References (41)
  • 1
    • 63249089562 scopus 로고    scopus 로고
    • Leucyl aminopeptidase A
    • Barrett,A.J, Rawlings,N.D. and Woessner,J.F, eds, 2nd edn, Academic Press, Washington, DC
    • Colloms,S.D. (2003) Leucyl aminopeptidase A. In Barrett,A.J., Rawlings,N.D. and Woessner,J.F. (eds), Handbook of Proteolytic Enzymes, 2nd edn., Academic Press, Washington, DC.
    • (2003) Handbook of Proteolytic Enzymes
    • Colloms, S.D.1
  • 2
    • 0024316734 scopus 로고
    • xerB, an Escherichia coli gene required for plasmid ColE1 site-specific recombination, is identical to pepA, encoding aminopeptidase A, a protein with substantial similarity to bovine lens leucine aminopeptidase
    • Stirling,C.J., Colloms,S.D., Collins,J.F., Szatmari,G. and Sherratt,D.J. (1989) xerB, an Escherichia coli gene required for plasmid ColE1 site-specific recombination, is identical to pepA, encoding aminopeptidase A, a protein with substantial similarity to bovine lens leucine aminopeptidase. EMBO J., 8, 1623-1627.
    • (1989) EMBO J , vol.8 , pp. 1623-1627
    • Stirling, C.J.1    Colloms, S.D.2    Collins, J.F.3    Szatmari, G.4    Sherratt, D.J.5
  • 3
    • 0342618313 scopus 로고    scopus 로고
    • Direct interaction of aminopeptidase A with recombination site DNA in Xer site-specific recombination
    • Alén,C., Sherratt,D.J. and Colloms,S.D. (1997) Direct interaction of aminopeptidase A with recombination site DNA in Xer site-specific recombination. EMBO J., 16, 5188-5197.
    • (1997) EMBO J , vol.16 , pp. 5188-5197
    • Alén, C.1    Sherratt, D.J.2    Colloms, S.D.3
  • 4
    • 0029146877 scopus 로고
    • carP, involved in pyrimidine regulation of the Escherichia coli carbamoylphosphate synthetase operon encodes a sequence-specific DNA-binding protein identical to XerB and PepA, also required for resolution of ColE1 multimers
    • Charlier,D., Hassanzadeh,G., Kholti,A., Gigot,D., Piérard,A. and Glansdorff,N. (1995) carP, involved in pyrimidine regulation of the Escherichia coli carbamoylphosphate synthetase operon encodes a sequence-specific DNA-binding protein identical to XerB and PepA, also required for resolution of ColE1 multimers. J. Mol. Biol., 250 392-406.
    • (1995) J. Mol. Biol , vol.250 , pp. 392-406
    • Charlier, D.1    Hassanzadeh, G.2    Kholti, A.3    Gigot, D.4    Piérard, A.5    Glansdorff, N.6
  • 5
    • 0028237249 scopus 로고
    • Peptidase activity of Escherichia coli aminopeptidase A is not required for its role in Xer site-specific recombination
    • McCulloch,R., Burke,M.E. and Sherratt,D. (1994) Peptidase activity of Escherichia coli aminopeptidase A is not required for its role in Xer site-specific recombination. Mol. Microbiol., 12, 241-251.
    • (1994) Mol. Microbiol , vol.12 , pp. 241-251
    • McCulloch, R.1    Burke, M.E.2    Sherratt, D.3
  • 6
  • 7
    • 0347761240 scopus 로고    scopus 로고
    • Purine and pyrimidine-specific repression of the Escherichia coli carAB operon are functionally and structurally coupled
    • Devroede,N., Thia-Toong,T.-L., Gigot,D., Maes,D. and Charlier,D. (2004) Purine and pyrimidine-specific repression of the Escherichia coli carAB operon are functionally and structurally coupled. J. Mol. Biol., 336, 25-42.
    • (2004) J. Mol. Biol , vol.336 , pp. 25-42
    • Devroede, N.1    Thia-Toong, T.-L.2    Gigot, D.3    Maes, D.4    Charlier, D.5
  • 8
    • 0029119534 scopus 로고
    • Pyrimidine regulation of the Escherichia coli and Salmonella typhimurium carAB operons: CarP and integration host factor (IHF) modulate the methylation status of a GATC site present in the control region
    • Charlier,D., Gigot,D., Huysveld,N., Roovers,M., Piérard,A. and Glansdorff,N. (1995) Pyrimidine regulation of the Escherichia coli and Salmonella typhimurium carAB operons: CarP and integration host factor (IHF) modulate the methylation status of a GATC site present in the control region. J. Mol. Biol., 250, 383-391.
    • (1995) J. Mol. Biol , vol.250 , pp. 383-391
    • Charlier, D.1    Gigot, D.2    Huysveld, N.3    Roovers, M.4    Piérard, A.5    Glansdorff, N.6
  • 9
    • 0027464788 scopus 로고
    • Integration host factor (IHF) modulates the expression of the pyrimidine-specific promoter of the carAB operons of Escherichia coli K12 and Salmonella typhimurium LT2
    • Charlier,D., Roovers,M., Gigot,D., Huysveld,N., Piérard,A. and Glansdorff,N. (1993) Integration host factor (IHF) modulates the expression of the pyrimidine-specific promoter of the carAB operons of Escherichia coli K12 and Salmonella typhimurium LT2. Mol. Gen. Genet., 237, 273-286.
    • (1993) Mol. Gen. Genet , vol.237 , pp. 273-286
    • Charlier, D.1    Roovers, M.2    Gigot, D.3    Huysveld, N.4    Piérard, A.5    Glansdorff, N.6
  • 10
    • 0032563126 scopus 로고    scopus 로고
    • pyrH-encoded UMP-kinase directly participates in pyrimidine-specific modulation of promoter activity in Escherichia coli
    • Kholti,A., Charlier,D., Gigot,D., Huysveld,N. and Glansdorff,N. (1998) pyrH-encoded UMP-kinase directly participates in pyrimidine-specific modulation of promoter activity in Escherichia coli. J. Mol. Biol., 280, 571-582.
    • (1998) J. Mol. Biol , vol.280 , pp. 571-582
    • Kholti, A.1    Charlier, D.2    Gigot, D.3    Huysveld, N.4    Glansdorff, N.5
  • 11
    • 35448941579 scopus 로고    scopus 로고
    • RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines
    • 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. Mocrobiol., 66 744-757.
    • (2007) Mol. Mocrobiol , vol.66 , pp. 744-757
    • Shimada, T.1    Hirao, K.2    Kori, A.3    Yamamoto, K.4    Ishihama, A.5
  • 12
    • 0029947260 scopus 로고    scopus 로고
    • Accessory proteins impose site selectivity during ColE1 dimer resolution
    • Guhathakurta,A., Viney,I. and Summers,D. (1996) Accessory proteins impose site selectivity during ColE1 dimer resolution. Mol. Microbiol., 20, 613-620.
    • (1996) Mol. Microbiol , vol.20 , pp. 613-620
    • Guhathakurta, A.1    Viney, I.2    Summers, D.3
  • 14
    • 0031979599 scopus 로고    scopus 로고
    • The ArcA/ArcB two-component regulatory system of Escherichia coli is essential for Xer site-specific recombination at psi
    • Colloms,S.D., Alén,C. and Sherratt,D.J. (1998) The ArcA/ArcB two-component regulatory system of Escherichia coli is essential for Xer site-specific recombination at psi. Mol. Microbiol., 28 521-530.
    • (1998) Mol. Microbiol , vol.28 , pp. 521-530
    • Colloms, S.D.1    Alén, C.2    Sherratt, D.J.3
  • 15
    • 0027422093 scopus 로고
    • Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12
    • Blakely,G., May,G., McCulloch,R., Arciszewska,L., Burke,M., Lovett,S. and Sherratt,D.J. (1993) Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12. Cell, 75, 351-361.
    • (1993) Cell , vol.75 , pp. 351-361
    • Blakely, G.1    May, G.2    McCulloch, R.3    Arciszewska, L.4    Burke, M.5    Lovett, S.6    Sherratt, D.J.7
  • 16
    • 1942455734 scopus 로고    scopus 로고
    • Control of Cre recombination by regulatory elements from Xer recombination systems
    • Gourlay,S.C. and Colloms,S.D. (2004) Control of Cre recombination by regulatory elements from Xer recombination systems. Mol. Microbiol. 52, 53-65.
    • (2004) Mol. Microbiol , vol.52 , pp. 53-65
    • Gourlay, S.C.1    Colloms, S.D.2
  • 17
    • 0037169328 scopus 로고    scopus 로고
    • FtsK is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases
    • Aussel,L., Barre,F.X., Aroyo,M., Stasiak,A.Z. and Sherrat,D.J. (2002) FtsK is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases. Cell, 108, 195-205.
    • (2002) Cell , vol.108 , pp. 195-205
    • Aussel, L.1    Barre, F.X.2    Aroyo, M.3    Stasiak, A.Z.4    Sherrat, D.J.5
  • 18
    • 0344931801 scopus 로고    scopus 로고
    • X-ray structure of aminopeptidase A from Escherichia coli and a model for the nucleoprotein complex in Xer site-specific recombination
    • Sträter,N., Sherratt,D.J. and Colloms,S.D. (1999) X-ray structure of aminopeptidase A from Escherichia coli and a model for the nucleoprotein complex in Xer site-specific recombination. EMBO J., 18, 4513-4522.
    • (1999) EMBO J , vol.18 , pp. 4513-4522
    • Sträter, N.1    Sherratt, D.J.2    Colloms, S.D.3
  • 20
    • 23744505065 scopus 로고    scopus 로고
    • Mutagenesis of PepA suggests a new model for the Xer/cer synaptic complex
    • Reijns,M., Lu,Y., Leach,S. and Colloms,S.D. (2005) Mutagenesis of PepA suggests a new model for the Xer/cer synaptic complex. Mol. Microbiol., 57, 927-941.
    • (2005) Mol. Microbiol , vol.57 , pp. 927-941
    • Reijns, M.1    Lu, Y.2    Leach, S.3    Colloms, S.D.4
  • 21
    • 0037328523 scopus 로고    scopus 로고
    • Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy
    • Yang,Y., Wang,H. and Erie,D. (2002) Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy. Methods, 29, 175-187.
    • (2002) Methods , vol.29 , pp. 175-187
    • Yang, Y.1    Wang, H.2    Erie, D.3
  • 22
    • 0348141036 scopus 로고    scopus 로고
    • Insights into the regulation of transcription by scanning force microscopy
    • Dame,R.T., Wyman,C. and Goosen,N. (2003) Insights into the regulation of transcription by scanning force microscopy. J. Microsc., 212 244-253.
    • (2003) J. Microsc , vol.212 , pp. 244-253
    • Dame, R.T.1    Wyman, C.2    Goosen, N.3
  • 23
  • 24
    • 33646230289 scopus 로고    scopus 로고
    • Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase
    • Devroede,N., Huysveld,N. and Charlier,D. (2006) Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. J. Bacteriol., 188, 3236-3245.
    • (2006) J. Bacteriol , vol.188 , pp. 3236-3245
    • Devroede, N.1    Huysveld, N.2    Charlier, D.3
  • 26
    • 26644455043 scopus 로고    scopus 로고
    • Dame,R.T., van Marmeren,J., Luijsterburg,M.S., Mysiak,M.E., Janicijevic,A., Pazdzior,G., van der Vliet,P.C., Wyman,C. and Wuite,G.J.L. (2005) Analysis of scanning force microscopy images of protein-induced DNA bending using simulations. Nucleic Acids Res., 33, e68; erratum (2005). Nucleic Acids Res., 33, 2767.
    • Dame,R.T., van Marmeren,J., Luijsterburg,M.S., Mysiak,M.E., Janicijevic,A., Pazdzior,G., van der Vliet,P.C., Wyman,C. and Wuite,G.J.L. (2005) Analysis of scanning force microscopy images of protein-induced DNA bending using simulations. Nucleic Acids Res., 33, e68; erratum (2005). Nucleic Acids Res., 33, 2767.
  • 27
    • 0033575742 scopus 로고    scopus 로고
    • Wrapping of DNA around the E. coli RNA polymerase open promoter complex
    • Rivetti,C., Guthold,M. and Bustamante,C. (1999) Wrapping of DNA around the E. coli RNA polymerase open promoter complex. EMBO J., 18, 4464-4475.
    • (1999) EMBO J , vol.18 , pp. 4464-4475
    • Rivetti, C.1    Guthold, M.2    Bustamante, C.3
  • 28
    • 0030596081 scopus 로고    scopus 로고
    • Scanning force microscopy of DNA deposited onto mica: Equilibration versus kinetic trapping studied by statistical polymer chain analysis
    • Rivetti,C., Guthold,M. and Bustamante,C. (1996) Scanning force microscopy of DNA deposited onto mica: Equilibration versus kinetic trapping studied by statistical polymer chain analysis. J. Mol. Biol. 264, 919-932.
    • (1996) J. Mol. Biol , vol.264 , pp. 919-932
    • Rivetti, C.1    Guthold, M.2    Bustamante, C.3
  • 30
    • 63249105883 scopus 로고    scopus 로고
    • An Lrp-type transcriptional regulator from Agrobacterium tumefaciens condenses more than 100 nucleotides of DNA into globular nucleoprotein complexes
    • Jafri,S., Chen,S. and Calvo,J.M. (1999) An Lrp-type transcriptional regulator from Agrobacterium tumefaciens condenses more than 100 nucleotides of DNA into globular nucleoprotein complexes. J. Bacteriol., 184, 5293-5300.
    • (1999) J. Bacteriol , vol.184 , pp. 5293-5300
    • Jafri, S.1    Chen, S.2    Calvo, J.M.3
  • 31
    • 33744954870 scopus 로고    scopus 로고
    • Ss-LrpB from Sulfolobus solfataricus condenses about 100 base pairs of its own operator DNA into globular nucleoprotein complexes
    • Peeters,E., Willaert,R., Maes,D. and Charlier,D. (2006) Ss-LrpB from Sulfolobus solfataricus condenses about 100 base pairs of its own operator DNA into globular nucleoprotein complexes. J. Biol. Chem. 281, 11721-11728.
    • (2006) J. Biol. Chem , vol.281 , pp. 11721-11728
    • Peeters, E.1    Willaert, R.2    Maes, D.3    Charlier, D.4
  • 32
    • 0030894489 scopus 로고    scopus 로고
    • Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein
    • Wyman,C., Rombel,I., North,A.K., Bustamante,C. and Kustu,S. (1997) Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein. Science, 275, 1658-1661.
    • (1997) Science , vol.275 , pp. 1658-1661
    • Wyman, C.1    Rombel, I.2    North, A.K.3    Bustamante, C.4    Kustu, S.5
  • 33
    • 0034814802 scopus 로고    scopus 로고
    • A novel single-molecule study to determine protein-protein association constants
    • Ratcliff,G.C. and Erie,D.A. (2001) A novel single-molecule study to determine protein-protein association constants. J. Am. Chem. Soc. 123, 5632-5635.
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 5632-5635
    • Ratcliff, G.C.1    Erie, D.A.2
  • 34
    • 0037022821 scopus 로고    scopus 로고
    • A minimal exonuclease domain of WRN forms a hexamer on DNA and possesses both 3′-5′ exonuclease and 5′-protruding strand endonuclease activities
    • Xue,Y., Ratcliff,G.C., Wang,H., Davis-Searles,P.R., Gray,M.D., Erie,D.A. and Redinbo,M.R. (2002) A minimal exonuclease domain of WRN forms a hexamer on DNA and possesses both 3′-5′ exonuclease and 5′-protruding strand endonuclease activities. Biochemistry, 41, 2901-2912.
    • (2002) Biochemistry , vol.41 , pp. 2901-2912
    • Xue, Y.1    Ratcliff, G.C.2    Wang, H.3    Davis-Searles, P.R.4    Gray, M.D.5    Erie, D.A.6    Redinbo, M.R.7
  • 36
    • 0038136948 scopus 로고    scopus 로고
    • Contribution of DNA conformation and topology in right-handed DNA wrapping by the Bacillus subtilis LrpC protein
    • Beloin,C., Jeusset,J., Révet,B., Mirambeau,G., Le Hégarat,F. and Le Cam,E. (2003) Contribution of DNA conformation and topology in right-handed DNA wrapping by the Bacillus subtilis LrpC protein. J. Biol. Chem., 278, 5333-5342.
    • (2003) J. Biol. Chem , vol.278 , pp. 5333-5342
    • Beloin, C.1    Jeusset, J.2    Révet, B.3    Mirambeau, G.4    Le Hégarat, F.5    Le Cam, E.6
  • 37
    • 0031951638 scopus 로고    scopus 로고
    • Regulation of carAB expression in Escherichia coli occurs in part through UTP-sensitive reiterative transcription
    • Han,X. and Turnbough,C.L. Jr. (1998) Regulation of carAB expression in Escherichia coli occurs in part through UTP-sensitive reiterative transcription. J. Bacteriol., 180, 705-713.
    • (1998) J. Bacteriol , vol.180 , pp. 705-713
    • Han, X.1    Turnbough Jr., C.L.2
  • 38
    • 0348183087 scopus 로고
    • Multiple regulatory signals in the control of the Escherichia coli carAB operon
    • Bouvier,J., Patte,J.C. and Stragier,P. (1984) Multiple regulatory signals in the control of the Escherichia coli carAB operon. Proc. Natl Acad. Sci. USA, 81, 4139-4143.
    • (1984) Proc. Natl Acad. Sci. USA , vol.81 , pp. 4139-4143
    • Bouvier, J.1    Patte, J.C.2    Stragier, P.3
  • 39
    • 21844477035 scopus 로고    scopus 로고
    • Structure of Escherichia coli UMP kinase differs from that of other NMP kinases and sheds new light on enzyme regulation
    • Briozzo,P., Evrin,C., Meyer,P., Assairi,L., Joly,N, Bârzu,O. and Gilles,A.M. (2005) Structure of Escherichia coli UMP kinase differs from that of other NMP kinases and sheds new light on enzyme regulation. J. Biol. Chem., 280, 25533-25540.
    • (2005) J. Biol. Chem , vol.280 , pp. 25533-25540
    • Briozzo, P.1    Evrin, C.2    Meyer, P.3    Assairi, L.4    Joly, N.5    Bârzu, O.6    Gilles, A.M.7
  • 40
    • 23944435947 scopus 로고    scopus 로고
    • The crystal structure of Pyrococcus furiosus UMP kinase provides insights into catalysis and regulation in microbial nucleotide biosynthesis
    • Marco-Marín,C., Gil-Otiz,F. and Rubio,V. (2005) The crystal structure of Pyrococcus furiosus UMP kinase provides insights into catalysis and regulation in microbial nucleotide biosynthesis. J. Mol. Biol. 352, 438-454.
    • (2005) J. Mol. Biol , vol.352 , pp. 438-454
    • Marco-Marín, C.1    Gil-Otiz, F.2    Rubio, V.3
  • 41
    • 33645802381 scopus 로고    scopus 로고
    • Self-control in DNA site-specific recombination mediated by the tyrosine recombinase TnpI
    • Vanhooff,V., Galloy,C., Agaisse,H., Lereclus,D., Révet,B. and Hallet,B. (2006) Self-control in DNA site-specific recombination mediated by the tyrosine recombinase TnpI. Mol. Microbiol., 60 617-629.
    • (2006) Mol. Microbiol , vol.60 , pp. 617-629
    • Vanhooff, V.1    Galloy, C.2    Agaisse, H.3    Lereclus, D.4    Révet, B.5    Hallet, B.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.