Composite
C1

Part:BBa_K3308083

Designed by: Jemy Varghese, Harrison Green, Ripal Sheth, Victor So, Mel Marciesky   Group: iGEM19_Pittsburgh   (2019-10-06)
Revision as of 01:34, 21 October 2019 by Jvargh (Talk | contribs)


[NrdJ-1 C (1-4)]-[Tvo VMA C48 N]

C1-construct

Overview

Coded- Nested intein diagram.png
The Pittsburgh iGEM team 2019 designed a modular protein circuit system consisting of split Intein-based logic gates. This composite part is an input of the proposed nested intein system. This system is composed of two-independent splicing events reconstituting function functional half of a nested intein. Each nested intein’s chain (N and C terminus) will be split at one location by another split intein rendering it nonfunctional. Consequently only splicing of the “inner inteins”, will reconstruct the functional intein that is fused to the desired extein. [5]In this system, the primary splicing events taking place at each split site of the nested intein halves, will serve an AND gate. Each AND is composed of two inputs, the N- and C- terminals of matching inteins.[1]
Figure 2: Nesting NrdJ-1 Inteins with gp41-1 and TvoVMA split inteins. This set of constructs is identical to BBa_K3308007-13; however,this this composite part contains a solubility tag (maltose binding protein) that is expected to aide in the solubilization of the parts inside the cell. The addition of this tag is said to decrease aggregation of proteins. [3]. This composite part contains the N-terminal of primary splicing intein, TvoVMA, on the C side. We have denoted it as the C1 construct. The N-Terminus of this split intein is fused to a split site we have chosen in the C-terminus of the intein NrdJ-1. In order to choose this split site we had to consider that the N-terminal flanking sequences for TvoVMA inteins.

Design

After expression and attempted purification of BBa_K3308009, We decided that we would conduct Gibson Assembly of the part into a different plasmid backbone BBa_K3308093 consisting of Maltose Binding Protein[3,5]. Maltose Bidning Protein is a relatively large 42 kDa This construct has the N terminus of TvoVMA Intein, it is covalently attached to the first half of the C-terminal NrdJ-1 InteinBBa_K3308070. The main purpose of this construct is to preserve functional splicing of TvoVma N intein.[1]

For TvoVMA we thought that it could better handle a C+2 change better than a N-1 change; therefore the TvoVMA was chosen to be put in this specific split site because the N and C flanking sequences on either side of the spliting site of NrdJ-1 C match what we expect is needed for efficient splicing.[3].

This construct was predicted to splice in the presence of its partner, BBa_K3308084, to form fully fucntional C-terminus NrdJ-1 (BBa_K3308086). If splicing occurs as planned between these two constructs then, addition of BBa_K3308083, BBa_K3308084, and BBa_K3308085 should result in the effective reconstruction of the full extein (GB1-GTNPC-SEIVL-gpD)- BBa_K3308087


Usage

Each construct of the set was labeled with 6XHis tag, for the purposes of purification via Ni-NTA resin(1ul/mL of culture). Following the His-tag the composite part also consists of a Tev7 Protease binding site, indicated the three dashed lines. It is important to note that the addition of the tag and cleavage site was not expected to have any impact on the splicing mechanisms of the intein.

This construct was induced and expected to react with BBa_K3308084 C2 to form the spliced product, the full terminus of the N- NrdJ-1 Intein CSP BBa_K3308086.

Results

We dececided to utilze the MBP tagged varient of this composite part. We were able to grow, express, and pruify this protein construct. Because this part was only the first few amino acids of the NrdJ-1 C terminal (due to the fact that we chose a split site that was closer to the N terminus of the C- Intein NrdJ-1), the construct did not as much of an issue purifying.

File:Purification 47 48 lysate.png
Figure 2: The SDS-Page gel above is a lysate mixture test combing lysate mictures of 47(BBa_K3308083 and 48 BBa_K3308084
In the very last column we cna see a clear

The following construct was tested for splicing of TvoVMA by combining lysates of this construct and BBa_K3308084. We were able to see efficient splicing of these two constructs and conclude the Nested C terminal NrdJ-1 was spliced together. We can clearly see the starting concentration of the two constructs, the depletion of of the starting intein constructs, and formation of the spliced product which is smaller in kDa.

ADD the PICTURE and description


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 408
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 1222
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 106

References

[1] Gramespacher, J. A., Stevens, A. J., Thompson, R. E., & Muir, T. W. (2018). Improved protein splicing using embedded split inteins. Protein Science, 27(3), 614–619. https://doi.org/10.1002/pro.3357

[2] Beyer, H.M., Mikula, K.M., Li, M.,Wlodawer, A., Iwai, H., (2019) The crystal structure of the naturally split gp41-1 intein guides the engineering of orthogonal split inteins from a cis-splicing intein.BioRxiv. https://doi.org/10.1101/546465

[3] Kimple, M. E., Brill, A. L., & Pasker, R. L. (2013). Overview of affinity tags for protein purification. Current protocols in protein science, 73, Unit–9.9. doi:10.1002/0471140864.ps0909s73

[4]  Amitai, G., Callahan, B. P., Stanger, M. J., Belfort, G., & Belfort, M. (2009). Modulation of intein activity by its neighboring extein substrates. Proceedings of the National Academy of Sciences, 106(27), 11005–11010. https://doi.org/10.1073/pnas.0904366106

[5] Costa, S., Almeida, A., Castro, A., & Domingues, L. (2014). Fusion tags for protein solubility, purification and immunogenicity in Escherichia coli: the novel Fh8 system. Frontiers in Microbiology, 5. doi: 10.3389/fmicb.2014.00063

[6] Shah, N. H., & Muir, T. W. (2014). Inteins: Nature’s gift to protein chemists. Chemical Science, 5(2), 446–461. https://doi.org/10.1039/c3sc52951g

[7] Øemig, J. S. (2013)Structural Studies on Intein. (Published Doctoral Dissertation). University of Helsinki. Helsinki, Finland Retrieved from https://pdfs.semanticscholar.org/3c6a/b9fa31488316df5f421869163101ba13037e.pdf

Contribution Markup

This page was was last updated by Pittsburgh 2019 team.

This part is this set of nested Inteins constructs: BBa_K3308082. BBa_K3308081. BBa_K3308084. BBa_K3308085. BBa_K3308086. BBa_K3308087.

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