Difference between revisions of "Part:BBa K3102044:Design"

Revision as of 08:36, 16 October 2019

Electron transfer improvement (ACS, ZWF, GND, PGL)

Assembly Compatibility:

10
INCOMPATIBLE WITH RFC[10]
Illegal PstI site found at 2933
12
INCOMPATIBLE WITH RFC[12]
Illegal PstI site found at 2933
Illegal NotI site found at 2814
21
INCOMPATIBLE WITH RFC[21]
Illegal BamHI site found at 3490
Illegal XhoI site found at 408
23
INCOMPATIBLE WITH RFC[23]
Illegal PstI site found at 2933
25
INCOMPATIBLE WITH RFC[25]
Illegal PstI site found at 2933
Illegal NgoMIV site found at 2206
Illegal NgoMIV site found at 2923
Illegal NgoMIV site found at 5493
Illegal AgeI site found at 837
Illegal AgeI site found at 4245
1000
INCOMPATIBLE WITH RFC[1000]
Illegal SapI.rc site found at 3975

Design Notes

In the ACS, we mutated a Cytosine into Thymine at the 1563bp position (C1563T) because of the Esp3I enzyme that we used for our Golden Gate Assembly (GGA) construct. (e.g BBa_K3102021)

In the ZWF, we mutated a Thymine into Cysteine at the 844bp position (T844C) because of the PstI enzyme (e.g. BBa_K3102008)

Source

AWS: E.coli, sequence found through Biocyc https://biocyc.org/gene?orgid=ECOLI&id=EG11448

ZWF: Corynebacterium glutamicum, sequence found through Ebi https://www.ebi.ac.uk/ena/data/view/BAB98969

GND: Corynebacterium glutamicum, sequence found through GenBank https://biocyc.org/gene?orgid=CORYNE&id=G18NG-11035-MONOMER#tab=TU

GLD: E.coli, sequence found through GenBank https://www.ncbi.nlm.nih.gov/nuccore/NC_000913.3?from=798586&to=799581&report=fasta

Promoter (BBa_I719005), RBS (BBa_B0034) and Terminator (BBa_B0015) are from the iGEM Registry.

References

Brown TD. et al., The enzymic interconversion of acetate and acetyl-coenzyme A in Escherichia coli, J Gen Microbiol. 1977 Oct;102(2):327-36.

Chen Y.Y. et al., "Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism.", J. Struct. Biol. 169:25-35(2010)

Kumari S. et al., Cloning, characterization, and functional expression of acs, the gene which encodes acetyl coenzyme A synthetase in Escherichia coli, J Bacteriol. 1995 May;177(10):2878-86.

Thomason L.C., Court D.L. et al., "Identification of the Escherichia coli K-12 ybhE gene as pgl, encoding 6-phosphogluconolactonase." Bacteriol. 186:8248-8253(2004)

Zhao J. et al., "Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate." Metab. Eng. 6:164-174(2004)

@@ Line 27: / Line 27: @@
 ===References===
-Bacher A. et al., "Riboflavin synthases of Bacillus subtilis. Purification and properties." Biol. Chem. 255:632-637(1980)
 Brown TD. et al., The enzymic interconversion of acetate and acetyl-coenzyme A in Escherichia coli, J Gen Microbiol. 1977 Oct;102(2):327-36.
 Chen Y.Y. et al., "Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism.", J. Struct. Biol. 169:25-35(2010)
-Eberhardt S.M.R. et al., J"Cloning, sequencing, mapping and hyperexpression of the ribC gene coding for riboflavin synthase of Escherichia coli." . Biochem. 242:712-719(1996)
 Kumari S. et al., Cloning, characterization, and functional expression of acs, the gene which encodes acetyl coenzyme A synthetase in Escherichia coli, J Bacteriol. 1995 May;177(10):2878-86.
-Lin Z, et al., "Metabolic engineering of Escherichia coli for the production of riboflavin". Microb Cell Fact. 2014;13(1):1–12.
 Thomason L.C., Court D.L. et al., "Identification of the Escherichia coli K-12 ybhE gene as pgl, encoding 6-phosphogluconolactonase." Bacteriol. 186:8248-8253(2004)
 Zhao J. et al., "Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate." Metab. Eng. 6:164-174(2004)
-Zhenquan Lin et al., “Metabolic engineering of Escherichia coli for the production of riboflavin," Microbial Cell Factories, 2014, 13:104.