Difference between revisions of "Part:BBa K1076003:Design"

 
(→‎References)
 
(2 intermediate revisions by 2 users not shown)
Line 7: Line 7:
  
 
===Design Notes===
 
===Design Notes===
−
We chosed this ORF 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.  
+
We chosed this ORF 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. Should also be assembled with promoter, RBS and terminator.
−
 
+
−
 
+
  
 
===Source===
 
===Source===
Line 16: Line 14:
  
 
===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 23:36, 27 September 2013


FadD, Long-chain-fatty-acid-CoA ligase


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 1477
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 1631
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 1210
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 163


Design Notes

We chosed this ORF 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. Should also be assembled with promoter, RBS and terminator.

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.