Part:BBa_K3308007

GB1-GTNPC-[NrdJ-1 N (1-4)]-[gp41-1 N]

Overview

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 composite part contains the N-terminal of primary splicing intein, gp41-1. We have denoted it as the N1 construct. The N-Terminus of this split intein is fused to a split site we have chosen in the N-terminus of a different intein, NrdJ-1. In order to choose this split site we had to consider that the N-terminal flanking sequences for gp41-1 inteins, as well as the predicted structure of the NrdJ-1 intein.

Design

This construct has the first half of the N-terminal NrdJ-1 Intein, which means that it is covalently attached to the N-terminal extein, GB1BBa_K3308065. In between the N-terminus and the extein we have inserted has consensus flanking sequences, GTNPC, that are published as essential to aiding splicing of NrdJ-1, once the whole terminal comes together forming.[2,3,4] The main purpose of this construct is to preserve functional splicing of gp41-1 intein.[1] We had to take in consideration that gp41-1 that although we were able to match the requisites for C terminal gp41-1 intein BBa_K3308008.

The N1 position, which corresponds to the last amino acid of NrdJ-1 did not match the original sequence reported to preserve functionality in have been predicted to need in order to preserve splicing. The N-2 amino acid was a Glycine so we assumed that the N-2 properties as EWG or EDG were not as important for this intein.[7] The N-1 intein was a Lysine so we thought that this particular intein might need the resonance and hindrance of this amino acid, however this site has been changed before and able to still produce splicing. When looking into the block B site of gp41-1, we saw that there were many acid and base amino acid since this block is involved in the first step as reviewed above we thought that it would be more important than the N-1 intein here. [2]

Considering these things and the fact that any percent yield would still be considered a success for our current methods we decided that this site would be a strong candidate for success.

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_K3308008 N2 to form the spliced product, the full terminus of the N- NrdJ-1 Intein NSP ( BBa_K3308011.

Results

Unfortunately, this part was unable to be Gibson Cloned correctly. Upon sequencing transformed colonies, this part was found to have nonsense mutation; it was re-cloned; however, were unable to transform.

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  INCOMPATIBLE WITH RFC[1000]

  Illegal BsaI.rc site found at 121
  Illegal SapI.rc site found at 421
  

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] Lockless, S. W., & Muir, T. W. (2009). Traceless protein splicing utilizing evolved split inteins. Proceedings of the National Academy of Sciences of the United States of America, 106(27), 10999–11004. https://doi.org/10.1073/pnas.0902964106

[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]  Appleby-Tagoe, J. H., Thiel, I. V., Wang, Y., Wang, Y., Mootz, H. D., & Liu, X. Q. (2011). Highly efficient and more general cis- and trans-splicing inteins through sequential directed evolution. Journal of Biological Chemistry, 286(39), 34440–34447. https://doi.org/10.1074/jbc.M111.277350

[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_K3308010. BBa_K3308008. BBa_K3308009. BBa_K3308011. BBa_K3308012. BBa_K3308013.