Difference between revisions of "Part:BBa K239001:Design"

Latest revision as of 19:24, 21 October 2009

Spy promoter, activated by Phosporylated CpxR, BaeR and Sigma70

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

Design Notes

Detect and remove possible restriction sites: XbaI, EcoRI, PstI, SpeI, AgeI, BamHI, BglII, NogMIV, NotI and XhoI. No restriction site had to be removed. Sequence starts 3 bp before the first BaeR binding site and ends 5 pb after the -10 box.

Source

Genomic sequence from biocyc, Escherichia coli K-12. Native unmodified sequence.

References

Baranova, N., and H. Nikaido (2002) The BaeSR two-component regulatory system activates transcription of the yegMNOB (mdtABCD) transporter gene cluster in Escherichia coli and increases its resistance to novobiocin and deoxycholate. J. Bacteriol. 184:4168–4176.

DiGiuseppe, P. A., and T. J. Silhavy (2003) Signal detection and target gene induction by the CpxRA two-component system. J. Bacteriol. 185:2432– 2440.

Hagenmaier, S., Stierhof, Y.D., and Henning, U. (1997) A new periplasmic protein of Escherichia coli which is synthesized in spheroplasts but not in intact cells. J Bacteriol 179: 2073–2076.

Kunihiko Nishino, Eiji Nikaido, and Akihito Yamaguchi (2007) Regulation of Multidrug Efflux Systems Involved in Multidrug and Metal Resistance of Salmonella enterica Serovar Typhimurium. JOURNAL OF BACTERIOLOGY, Dec. 2007, p. 9066–9075

Nishino, K., T. Honda, and A. Yamaguchi. (2005) Genome-wide analyses of Escherichia coli gene expression responsive to the BaeSR two-component regulatory system. J. Bacteriol. 187:1763–1772.

Price, N. L., and T. L. Raivio. (2009) Characterization of the Cpx Regulon in Escherichia coli Strain MC4100 JOURNAL OF BACTERIOLOGY, Mar. 2009, p. 1798–1815

Raffa, R. G., and T. L. Raivio. (2002) A third envelope stress signal transduction pathway in Escherichia coli. Mol. Microbiol. 45:1599–1611.

Raivio, T. L., M. W. Laird, J. C. Joly, and T. J. Silhavy. (2000) Tethering of CpxP to the inner membrane prevents spheroplast induction of the cpx envelope stress response. Mol. Microbiol. 37:1186–1197.

Snyder, Larry., and Wendy Champness. (2007) Molecular genetics of bacteria, 3rd ed. ASM Press. Washington, DC.

Wulf, P.D., McGuire, A.M., Liu, X., and Lin, E.C.C. (2002) Genome-wide profiling of promoter recognition by the twocomponent response regulator CpxR-P in Escherichia coli. J Biol Chem 277: 26652–26661.

Yamamoto, K., Ishihama, A. (2005) Transcriptional response of Escherichia coli to external copper. Mol. Microbiol. 56, 215–227.

Yamamoto K, Ogasawara H, Ishihama A (2008) "Involvement of multiple transcription factors for metal-induced spy gene expression in Escherichia coli." J Biotechnol 133(2):196-200. PMID: 17884222

@@ Line 7: / Line 7: @@
 ===Design Notes===
 Detect and remove possible restriction sites: XbaI, EcoRI, PstI, SpeI, AgeI, BamHI, BglII, NogMIV, NotI and XhoI. No restriction site had to be removed. Sequence starts 3 bp before the first BaeR binding site and ends 5 pb after the -10 box.
 ===Source===
@@ Line 15: / Line 13: @@
 ===References===
-The BaeSR two-component regulatory system mediates resistance to condensed tannins in Escherichia coli.
-Zoetendal EG, Smith AH, Sundset MA, Mackie RI. 2008
+Baranova, N., and H. Nikaido (2002) The BaeSR two-component regulatory
-Appl Environ Microbiol. 2008 Jan;74(2):535-9. Epub 2007 Nov 26.
+system activates transcription of the yegMNOB (mdtABCD) transporter gene
+cluster in Escherichia coli and increases its resistance to novobiocin and
+deoxycholate. J. Bacteriol. 184:4168–4176.
+DiGiuseppe, P. A., and T. J. Silhavy (2003) Signal detection and target gene
+induction by the CpxRA two-component system. J. Bacteriol. 185:2432–
+.
+Hagenmaier, S., Stierhof, Y.D., and Henning, U. (1997) A
+new periplasmic protein of Escherichia coli which is synthesized
+in spheroplasts but not in intact cells. J Bacteriol
+: 2073–2076.
+Kunihiko Nishino, Eiji Nikaido, and Akihito Yamaguchi (2007) Regulation of Multidrug Efflux Systems Involved in Multidrug and
+Metal Resistance of Salmonella enterica Serovar Typhimurium. JOURNAL OF BACTERIOLOGY, Dec. 2007, p. 9066–9075
+Nishino, K., T. Honda, and A. Yamaguchi. (2005) Genome-wide analyses of
+Escherichia coli gene expression responsive to the BaeSR two-component
+regulatory system. J. Bacteriol. 187:1763–1772.
+Price, N. L., and T. L. Raivio. (2009) Characterization of the Cpx Regulon in Escherichia coli Strain MC4100
+JOURNAL OF BACTERIOLOGY, Mar. 2009, p. 1798–1815
+Raffa, R. G., and T. L. Raivio. (2002) A third envelope stress signal transduction
+pathway in Escherichia coli. Mol. Microbiol. 45:1599–1611.
+Raivio, T. L., M. W. Laird, J. C. Joly, and T. J. Silhavy. (2000) Tethering of
+CpxP to the inner membrane prevents spheroplast induction of the cpx
+envelope stress response. Mol. Microbiol. 37:1186–1197.
+Snyder, Larry., and Wendy Champness. (2007) Molecular genetics of bacteria, 3rd ed.
+ASM Press. Washington, DC.
+Wulf, P.D., McGuire, A.M., Liu, X., and Lin, E.C.C. (2002)
+Genome-wide profiling of promoter recognition by the twocomponent
+response regulator CpxR-P in Escherichia coli.
+J Biol Chem 277: 26652–26661.
+Yamamoto, K., Ishihama, A. (2005) Transcriptional response of Escherichia
+coli to external copper. Mol. Microbiol. 56, 215–227.
+Yamamoto K, Ogasawara H, Ishihama A (2008) "Involvement of multiple transcription factors for metal-induced spy gene expression in Escherichia coli." J Biotechnol 133(2):196-200. PMID: 17884222