Difference between revisions of "Part:BBa K1076002:Design"

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===Design Notes===
 
===Design Notes===
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We chosed the full lenght gene to be expressed into Shewanella putrefaciens making a super expression since the bacteria already have one copy of this gene in its genome. We made the primers pair with EcoR1 (5') and Pst1 (3') ends in order to clone into pSB1C3. Further subclonning and expression should be done within pSB3C5-152001.
+
We chosed the full lenght gene to be expressed into Shewanella putrefaciens making a super expression since the bacteria already have one copy of this gene in its genome. We made the primers pair with EcoR1 (5') and Pst1 (3') ends in order to clone into pSB1C3. Further subclonning and expression should be done within pSB3C5.
  
 
===Source===
 
===Source===
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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.
 +
 +
SCHAFFER, Jean E.; LODISH, Harvey F. Expression cloning and characterization of a novel adipocyte long chain fatty acid transport protein.Cell, v. 79, n. 3, p. 427-436, 1994.
 +
 +
 +
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.
 +
 +
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.
 +
 +
 +
MYERS, C. R.; MYERS, J. M. Replication of plasmids with the p15A origin in Shewanella putrefaciens MR‐1. Letters in applied microbiology, v. 24, n. 3, p. 221-225, 1997.
 +
 +
BLACK, Paul N. Primary sequence of the Escherichia coli fadL gene encoding an outer membrane protein required for long-chain fatty acid transport. Journal of bacteriology, v. 173, n. 2, p. 435-442, 1991.
 +
 +
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.
 +
 +
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.

Latest revision as of 23:35, 27 September 2013


FadL, Long-chain fatty acid outer membrane transporte


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 157
    Illegal PstI site found at 288
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 157
    Illegal PstI site found at 288
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 1021
    Illegal BamHI site found at 1765
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 157
    Illegal PstI site found at 288
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 157
    Illegal PstI site found at 288
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

We chosed the full lenght gene to be expressed into Shewanella putrefaciens making a super expression since the bacteria already have one copy of this gene in its genome. We made the primers pair with EcoR1 (5') and Pst1 (3') ends in order to clone into pSB1C3. Further subclonning and expression should be done within pSB3C5.

Source

From Shewanella putrefaciens 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.

SCHAFFER, Jean E.; LODISH, Harvey F. Expression cloning and characterization of a novel adipocyte long chain fatty acid transport protein.Cell, v. 79, n. 3, p. 427-436, 1994.


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.

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.


MYERS, C. R.; MYERS, J. M. Replication of plasmids with the p15A origin in Shewanella putrefaciens MR‐1. Letters in applied microbiology, v. 24, n. 3, p. 221-225, 1997.

BLACK, Paul N. Primary sequence of the Escherichia coli fadL gene encoding an outer membrane protein required for long-chain fatty acid transport. Journal of bacteriology, v. 173, n. 2, p. 435-442, 1991.

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.

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.