Difference between revisions of "Part:BBa K3308012"

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	__NOTOC__		__NOTOC__
	<partinfo>BBa_K3308012 short</partinfo>		<partinfo>BBa_K3308012 short</partinfo>
		+	===CSP-construct===
		+	===Overview===
		+	[[File:Coded- Nested intein diagram.png|300px|thumb|right| ]] 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. [[#References|[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.[[#References|[1]]]
−	full c side extein and c extein	+	[[File:pvs000028-34.png|900px|thumb|center|'''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 CSP construct. This costruct acts a positive control of splicing of TwoVMA ]]
		+
		+	===Design===
		+	This composite part contains the N-terminal of primary splicing intein, gp41-1. We have denoted it as the NSP construct. This costruct acts a positive control of splicing of gp41-1 (<partinfo>BBa_K3308007</partinfo> and <partinfo>BBa_K3308008</partinfo>). The part is the full NrdJ-1 N intein containing the total 104 amino acids. The extein we have inserted still has a consensus flanking sequences, SEIVL-gpD, the same as <partinfo>BBa_K3308010</partinfo>.[[#References|[2,3,4]]]
		+
		+	This part is the expected product of functional splicing of TvoVMA.[[#References|[4, 5]]] We also constructe this part to be able to test the when one the intein terminals is split, it can be added in solution with the full compliment to get functional reconstitution of the extein sequences <partinfo>BBa_K3308011</partinfo>.
		+
		+
		+	===Usage===
		+	The main purpose of this part was to act as a positive control for splicing of composite parts <partinfo>BBa_K3308009</partinfo> and <partinfo>BBa_K3308010</partinfo> and also a functional N-intein NrdJ-1 that should be able to splice with the spliced product of <partinfo>BBa_K3308007</partinfo> and <partinfo>BBa_K3308008</partinfo> ( aka. CSP-<partinfo>BBa_K3308011</partinfo> )
		+
		+	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.
		+
		+
		+	===Results===
		+
		+	===Results===
		+	Early on the expression and attempted purifications of this contruct, we noticed that levels were extremely low. There were low amount fo expression in comparison to constructs in the same nested inteins set. We found that many other intein researchers have found that the C- side of intein N ans C terminals are much more disordered [6].
		+
		+	[[File:purification_30_34.png|200px|thumb|right|'''Figure 2: Purification of K3308009( 30) and K3308010 (31)''' The above gel is a SDS-PAGE of the steps of purification. P- Pellet, S- Supernatant, Ft- Flowthrough, W-Wash(in sequential order), E- Elution] construct 33 corresponds with this composite part, there is no protein in our elution, and all of the protein has aggregated within the pellet ]]
		+
		+	The elution has very minimal to no protein in two type of lysis. Almsot all of the protein of interest was lost in the Pellet lane indicated in Figure 2 and 3. We concluded that this might mean that the disordered structure of C terminus of inteins (gp41-1-C and fully constructed NrdJ-1 C intein-CSP [6]. In presence of lysing and purifiation reagents, this C2 construct likely formed inclusion bodies(Insouble-therefore would show in the pellet).
		+
		+	Inorder to test whether lysis was the main issue contributing to why there was such little protein, we conducted a comparison between Emulsiflex lysis method versus our standard sonciation protocol. Figure 3, you can see although we optimized lysis, all of the protein remained in the pellet, indicating that formation of inclusion bodies was the main issue.
		+
		+	In response to C-terminal Intein insolubility, we decide to replicate these constructs into pTEV6/pKLD66 plasmid backbone <partinfo>BBa_K3308093</partinfo> containing Maltose binding protein. Addition of maltose binding protein is found to increase the solubility of C-terminal inteins. This part is exactly the same as partinfo>BBa_K3308084</partinfo> ; however that MBP has been added to the N-terminus of the C2 Construct.
		+
		+	[[File:purification_31_33.png|300px|thumb|left|'''Figure 2: Purification of K3308010( 31) and K3308012 (33)''' The SDS-PAGE of the steps of purification. P- Pellet, S- Supernatant, Ft- Flowthrough, W-Wash(in sequential order), E- Elution] Almost all of the expressed protein, showing as the dark top band in the pellet, came of the pellet meaning that we were unable to solubilize the protein. ]]
		+
		+	[[File:purification emulsiflex_31_33.png|300px|thumb|right|'''Figure 3: Purification via Emulsiflex of K3308010( 31) and K3308012 (33)''' this Figure is identical in lane composition as figure 2; P- Pellet, S- Supernatant, Ft- Flowthrough, W-Wash(in sequential order), E- Elution]. Even though lysis protocol were optimized, all the of protein came off in the Pellet. ]]
		+
		+	The results from Figure 2 and 3, were a major component to the evolution of our contructs. The insolubility of the C-terminals drastically impacted whether or not we were able to isolate the protein in buffer. We find that there is good expression of the C terminal inteins in our nested system; the best way to visualize their presence and activity with its corresponding N terminal had to be in Lysate mixture. Consequentially, there was a lot of noise in the gels.
−	<!-- Add more about the biology of this part here
−	===Usage and Biology===
	<!-- -->		<!-- -->
−	<span class='h3bb'>Sequence and Features</span>
	<partinfo>BBa_K3308012 SequenceAndFeatures</partinfo>		<partinfo>BBa_K3308012 SequenceAndFeatures</partinfo>
		+	===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
−	<!-- Uncomment this to enable Functional Parameter display	+	[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
−	===Functional Parameters===	+
−	<partinfo>BBa_K3308012 parameters</partinfo>	+	[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:
		+	<partinfo>BBa_K3308007</partinfo>.
		+	<partinfo>BBa_K3308008</partinfo>.
		+	<partinfo>BBa_K3308009</partinfo>.
		+	<partinfo>BBa_K3308010</partinfo>.
		+	<partinfo>BBa_K3308011</partinfo>.
		+	<partinfo>BBa_K3308013</partinfo>.

---

Revision as of 22:22, 20 October 2019

[NrdJ-1 C (1-4)]-[NrdJ-1 C (5-41)]-SEIVL-gpD

CSP-construct

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]

Design

This composite part contains the N-terminal of primary splicing intein, gp41-1. We have denoted it as the NSP construct. This costruct acts a positive control of splicing of gp41-1 (BBa_K3308007 and BBa_K3308008). The part is the full NrdJ-1 N intein containing the total 104 amino acids. The extein we have inserted still has a consensus flanking sequences, SEIVL-gpD, the same as BBa_K3308010.[2,3,4]

This part is the expected product of functional splicing of TvoVMA.[4, 5] We also constructe this part to be able to test the when one the intein terminals is split, it can be added in solution with the full compliment to get functional reconstitution of the extein sequences BBa_K3308011.

Usage

The main purpose of this part was to act as a positive control for splicing of composite parts BBa_K3308009 and BBa_K3308010 and also a functional N-intein NrdJ-1 that should be able to splice with the spliced product of BBa_K3308007 and BBa_K3308008 ( aka. CSP-BBa_K3308011 )

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.

Results

Results

Early on the expression and attempted purifications of this contruct, we noticed that levels were extremely low. There were low amount fo expression in comparison to constructs in the same nested inteins set. We found that many other intein researchers have found that the C- side of intein N ans C terminals are much more disordered [6].

The elution has very minimal to no protein in two type of lysis. Almsot all of the protein of interest was lost in the Pellet lane indicated in Figure 2 and 3. We concluded that this might mean that the disordered structure of C terminus of inteins (gp41-1-C and fully constructed NrdJ-1 C intein-CSP [6]. In presence of lysing and purifiation reagents, this C2 construct likely formed inclusion bodies(Insouble-therefore would show in the pellet).

Inorder to test whether lysis was the main issue contributing to why there was such little protein, we conducted a comparison between Emulsiflex lysis method versus our standard sonciation protocol. Figure 3, you can see although we optimized lysis, all of the protein remained in the pellet, indicating that formation of inclusion bodies was the main issue.

In response to C-terminal Intein insolubility, we decide to replicate these constructs into pTEV6/pKLD66 plasmid backbone BBa_K3308093 containing Maltose binding protein. Addition of maltose binding protein is found to increase the solubility of C-terminal inteins. This part is exactly the same as partinfo>BBa_K3308084</partinfo> ; however that MBP has been added to the N-terminus of the C2 Construct.

The results from Figure 2 and 3, were a major component to the evolution of our contructs. The insolubility of the C-terminals drastically impacted whether or not we were able to isolate the protein in buffer. We find that there is good expression of the C terminal inteins in our nested system; the best way to visualize their presence and activity with its corresponding N terminal had to be in Lysate mixture. Consequentially, there was a lot of noise in the gels.

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_K3308007. BBa_K3308008. BBa_K3308009. BBa_K3308010. BBa_K3308011. BBa_K3308013.