Coding

Part:BBa_K2560261

Designed by: Daniel Marchal   Group: iGEM18_Marburg   (2018-09-30)
Revision as of 21:59, 12 October 2018 by Marchal (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)


mcrC - C-terminal domain of Malonyl-CoA Reductase from Chloroflexus aurantiacus

This part contains the 3' part of the mcr gene for Malony-CoA Reductase from C. aurantiacus, encoding the C-terminal domain. This enzyme is involved in the 3-hydroxypropionate cycle for CO2 fixation and converts malonyl-CoA into 3-hydroxypropionic acid (Strauss & Fuchs, 1993). In a two-step reaction malonyl-CoA is first reduced to 3-oxopropanoic acid and then further reduced to 3-hydroxypropionic acid. The C-terminal domain catalyzes the first reaction step to 3-oxopropanoic acid and the N-terminal domain catalyzes the second reaction step to 3-hydroxypropionic acid.

BBa K2560260 Mcr pathway.png

It was shown that a splitted version of Mcr with separated C- and N-terminal domains increases enzyme activity (Liu et al., 2013). If these splitted genes shall be used take BBa_K2560262 and this part. If the gene for the whole enzyme shall be used take BBa_K2560260.

For this part, mcrC was codonoptimized for V. natriegens and then synthetisized and integrated into the vector BBa_K2560002 via BsmBI. It is part of the Marburg Toolbox, a golden gate based system für modular cloning. According to Liu et al, we designed the part so that McrN contains amino acid 1-549 of the overall protein and McrC amino acid 550-1219 (Liu et al., 2013).

Further down, an overview of the Marburg Toolbox is shown. Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 288
    Illegal NheI site found at 1690
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 361
    Illegal NgoMIV site found at 1975
    Illegal AgeI site found at 1524
  • 1000
    COMPATIBLE WITH RFC[1000]


Marburg Toolbox

We proudly present the Marburg Collection, a novel golden-gate-based toolbox containing various parts that are compatible with the PhytoBrick system and MoClo. Compared to other bacterial toolboxes, the Marburg Collection shines with superior flexibility. We overcame the rigid paradigm of plasmid construction - thinking in fixed backbone and insert categories - by achieving complete de novo assembly of plasmids.

36 connectors facilitate flexible cloning of multigene constructs and even allow for the inversion of individual transcription units. Additionally, our connectors function as insulators to avoid undesired crosstalk.

The Marburg Collection contains 123 parts in total, including:
inducible promoters, reporters, fluorescence and epitope tags, oris, resistance cassettes and genome engineering tools. To increase the value of the Marburg Collection, we additionally provide detailed experimental characterization for V. natriegens and a supportive software. We aspire availability of our toolbox for future iGEM teams to empower accelerated progression in their ambitious projects.


Figure 3: Hierarchical cloning is facilitated by subsequent Golden Gate reactions.
Basic building blocks like promoters or terminators are stored in level 0 plasmids. Parts from each category of our collection can be chosen to built level 1 plasmids harboring a single transcription unit. Up to five transcription units can be assembled into a level 2 plasmid.
Figure 4: Additional bases and fusion sites ensure correct spacing and allow tags.
Between some parts, additional base pairs were integrated to ensure correct spacing and to maintain the triplet code. We expanded our toolbox by providing N- and C- terminal tags by creating novel fusions and splitting the CDS and terminator part, respectively.


Parts of the Marburg Toolbox




Tags and Entry Vectors




  • K2560001 (Entry Vector with RFP dropout)
  • K2560002 (Entry Vector with GFP dropout)
  • K2560005 (Resistance Entry Vector with RFP Dropout)
  • K2560006 (Resistance Entry Vector with GFP Dropout)
  • K2560305 (gRNA Entry Vector with GFP Dropout)
[edit]
Categories
Parameters
None