Difference between revisions of "Part:BBa K1076000:Design"

(→‎Design Notes)
(→‎References)
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===References===
 
===References===
 +
SIMONS, Robert Walter et al. Regulation of fatty acid degradation in Escherichia coli: isolation and characterization of strains bearing insertion and temperature-sensitive mutations in gene fadR. Journal of bacteriology, v. 142, n. 2, p. 621-632, 1980.
 +
 +
HUGHES, KELLY T.; SIMONS, R. W.; NUNN, W. D. Regulation of fatty acid degradation in Escherichia coli: fadR superrepressor mutants are unable to utilize fatty acids as the sole carbon source. Journal of bacteriology, v. 170, n. 4, p. 1666-1671, 1988.
 +
 +
HEIDELBERG, John F. et al. Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. Nature biotechnology, v. 20, n. 11, p. 1118-1123, 2002.
 +
 +
XU, Yibin et al. The FadR· DNA Complex TRANSCRIPTIONAL CONTROL OF FATTY ACID METABOLISM INESCHERICHIA COLI. Journal of Biological Chemistry, v. 276, n. 20, p. 17373-17379, 2001.
 +
 +
ROBINSON, Lee T. Fatty Acid Metabolic Engineering: Insights for Bacterial Hydrocarbon Production. 2012. Doctor tese UNIVERSITY OF MINNESOTA.
 +
 +
VAGNER, Valerie; DERVYN, Etienne; EHRLICH, S. Dusko. A vector for systematic gene inactivation in Bacillus subtilis. Microbiology, v. 144, n. 11, p. 3097-3104, 1998.
 +
ZHANG, Youming et al. A new logic for DNA engineering using recombination in Escherichia coli. Nature genetics, v. 20, n. 2, p. 123-128, 1998.
 +
 +
KAZAKOV, Alexey E. et al. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. Journal of bacteriology, v. 191, n. 1, p. 52-64, 2009.
 +
 +
MORGAN-KISS, Rachael M.; CRONAN, John E. The Escherichia coli fadK (ydiD) gene encodes an anerobically regulated short chain acyl-CoA synthetase. Journal of Biological Chemistry, v. 279, n. 36, p. 37324-37333, 2004.
 +
 +
CLARK, DAVID. Regulation of fatty acid degradation in Escherichia coli: analysis by operon fusion. Journal of bacteriology, v. 148, n. 2, p. 521-526, 1981.
 +
 +
RODIONOV, Dmitry A. et al. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC genomics, v. 12, n. Suppl 1, p. S3, 2011.
 +
 +
FUJITA, Yasutaro; MATSUOKA, Hiroshi; HIROOKA, Kazutake. Regulation of fatty acid metabolism in bacteria. Molecular microbiology, v. 66, n. 4, p. 829-839, 2007.
 +
 +
CHO, Byung-Kwan; KNIGHT, Eric M.; PALSSON, Bernhard Ø. Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. Microbiology, v. 152, n. 8, p. 2207-2219, 2006.
 +
 +
EVANS, W. Charles; FUCHS, G. Anaerobic degradation of aromatic compounds. Annual Reviews in Microbiology, v. 42, n. 1, p. 289-317, 1988.

Revision as of 23:23, 27 September 2013


fatty acid metabolism regulator protein FadR


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 536
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

It was design taking in consideration we had to put in a conjugative plasmid (pNPTS138) in E. coli and further on trasform Shewanella putrefaciens by conjugation. To put into pNPTS138 we used primers with Apa1(5') and BamH1(3')ends. After in order to put into pSB1C3 we clonned it in Topo plasmids and cut with Xba1 and Spe1 to further ligation on pSB1C3.

Source

It comes from amplified genomic sequence

References

SIMONS, Robert Walter et al. Regulation of fatty acid degradation in Escherichia coli: isolation and characterization of strains bearing insertion and temperature-sensitive mutations in gene fadR. Journal of bacteriology, v. 142, n. 2, p. 621-632, 1980.

HUGHES, KELLY T.; SIMONS, R. W.; NUNN, W. D. Regulation of fatty acid degradation in Escherichia coli: fadR superrepressor mutants are unable to utilize fatty acids as the sole carbon source. Journal of bacteriology, v. 170, n. 4, p. 1666-1671, 1988.

HEIDELBERG, John F. et al. Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. Nature biotechnology, v. 20, n. 11, p. 1118-1123, 2002.

XU, Yibin et al. The FadR· DNA Complex TRANSCRIPTIONAL CONTROL OF FATTY ACID METABOLISM INESCHERICHIA COLI. Journal of Biological Chemistry, v. 276, n. 20, p. 17373-17379, 2001.

ROBINSON, Lee T. Fatty Acid Metabolic Engineering: Insights for Bacterial Hydrocarbon Production. 2012. Doctor tese UNIVERSITY OF MINNESOTA.

VAGNER, Valerie; DERVYN, Etienne; EHRLICH, S. Dusko. A vector for systematic gene inactivation in Bacillus subtilis. Microbiology, v. 144, n. 11, p. 3097-3104, 1998. 

ZHANG, Youming et al. A new logic for DNA engineering using recombination in Escherichia coli. Nature genetics, v. 20, n. 2, p. 123-128, 1998.

KAZAKOV, Alexey E. et al. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. Journal of bacteriology, v. 191, n. 1, p. 52-64, 2009.

MORGAN-KISS, Rachael M.; CRONAN, John E. The Escherichia coli fadK (ydiD) gene encodes an anerobically regulated short chain acyl-CoA synthetase. Journal of Biological Chemistry, v. 279, n. 36, p. 37324-37333, 2004.

CLARK, DAVID. Regulation of fatty acid degradation in Escherichia coli: analysis by operon fusion. Journal of bacteriology, v. 148, n. 2, p. 521-526, 1981.

RODIONOV, Dmitry A. et al. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC genomics, v. 12, n. Suppl 1, p. S3, 2011.

FUJITA, Yasutaro; MATSUOKA, Hiroshi; HIROOKA, Kazutake. Regulation of fatty acid metabolism in bacteria. Molecular microbiology, v. 66, n. 4, p. 829-839, 2007.

CHO, Byung-Kwan; KNIGHT, Eric M.; PALSSON, Bernhard Ø. Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. Microbiology, v. 152, n. 8, p. 2207-2219, 2006.

EVANS, W. Charles; FUCHS, G. Anaerobic degradation of aromatic compounds. Annual Reviews in Microbiology, v. 42, n. 1, p. 289-317, 1988.