Difference between revisions of "Part:BBa K4719019"

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CBD-ProThr box-AnCDA chitin deacetylase and cellulose binding domain fusion protein
Sequence and Features

Introduction

Vilnius-Lithuania iGEM 2023 team's goal was to create synthetic biology tools for in vivo alterations of Komagataeibacter xylinus bacterial cellulose polymer composition. Firstly, we chose to produce a cellulose-chitin polymer that would later be deacetylated, creating bacterial cellulose-chitosan. This polymer is an easily modifiable platform when compared to bacterial cellulose. The enhanced chemical reactivity of the bacterial cellulose-chitosan polymer allows for specific functionalizations in the biomedicine field, such as scaffold design. As a second approach, we designed indigo-dyed cellulose that could be used as a green chemistry way to apply cellulose in the textile industry. Lastly, we have achieved a composite of bacterial cellulose and polyhydroxybutyrate (PHB), which is synthesized by K. xylinus.

Bacterial cellulose-chitin polymer was achieved by increasing the production of UDP-N-acetylglucosamine, which can be recognized as a viable substrate for cellulose synthase and incorporated in the bacterial cellulose polymer. We employed two strategies to produce this material. The first approach was to add N-acetylglucosamine into the growth medium BBa_K4719013, and the second one was the production of N-acetylglucosamine by K. xylinus from simple sugars such as glucose, fructose, and saccharose in the growth medium BBa_K4719014. After achieving bacterial cellulose-chitin copolymer, we had to deacetylase this material to produce bacterial cellulose-chitosan copolymer.

Usage and biology

This construct contains a fused cellulose binding domain connected to a linker to the N-terminus of deacetylase AnCDA BBa_K4719011 to ensure a higher degree of deacetylation. For protein purification, 6x his-tag was added to the N-terminus of the cellulose binding domain. The composite is contained in pBAD/HisB plasmid. For this part to be functional in your bacterial cellulose-chitosan copolymer production system, we had to purify recombinant protein coded by this composite. This part is used to produce bacterial cellulose-chitosan copolymer from bacterial cellulose-chitin copolymer via deacetylation.

Bacterial cellulose-chitosan copolymer has applications in the biomedicine field due to in vivo biodegradability by the lysosome. What is more, the bacterial cellulose-chitosan copolymer is a convenient platform for further modifications that would aid in solving the need for the promotion of tissue development. The uncovered amino groups are susceptible to enzymes catalyzing an addition of targeted organic chemistry groups. For instance, after modifying reaction conditions, deacetylase ClCDA BBa_K4719024 can propylate chitosan, which can later be used for click chemistry reactions [1]. In the future, specific targets like drugs or amino acids could be linked to the polymer, promoting the healing properties of the material [2].

Experimental characterization

Protein expression

Fusion with CBDcenA significantly decreased the solubility of deacetylases. To increase protein stability, we employed E. coli ArcticExpress (DE3) which is adapted for protein expression in lower temperatures. Investigating different biosynthesis conditions in ArcticExpress (DE3) revealed that induction at OD600 0.8 and growing the cells overnight at 16°C is optimal for fusion protein production.

Deacetylation enzymatic activity analysis with fluorescence microscopy

Deacetylation was performed in a reaction with a final volume of 200 µL: 2 µL 1 mM CoCl2, deacetylase CBD-ProThr box-AnCDA 100 nM - 2µM and filling the remaining volume with 20mM HEPES-NaOH ph8, 150mM NaCL buffer. The samples were incubated for 14 h at 37° while shaking at 300 rpm, reaction was stopped by incubating for 3 min at 98°C.

For cellulose-chitosan copolymer generation from cellulose-chitin exopolymer we used chitin deacetylase CBD-ProThr box-AnCDA. To determine if the deacetylation of our cellulose-chitin copolymer was successful, we used Alexa Fluor™ 405 NHS ester dye that specifically binds to free amino groups. On that account, only deacetylated copolymers should produce any fluorescent signal at this wavelength. To verify that our purified deacetylases are enzymatically active, at first we checked deacetylation activity on enzymes natural substrate - chitin.

Protein expression of recombinant deacetylase containing a new linker

A new linker BBa_K4719023 generated by our software was cloned into the pNIC-CH-6His-CBDCenA-AnCDA backbone by Gibson assembly. Investigating different biosynthesis conditions in ArcticExpress (DE3) revealed that induction at OD600 0.8 and growing the cells overnight at 16°C is optimal for fusion protein production.

Deacetylation enzymatic activity analysis with fluorescence microscopy

Deacetylation was performed in a reaction with a final volume of 200 µL: 2 µL 1 mM CoCl2, deacetylase CBD-FRF-AnCDA 50 nM - 2µM and filling the remaining volume with 20mM HEPES-NaOH ph8, 150mM NaCL buffer. The samples were incubated for 14 h at 37° while shaking at 300 rpm, reaction was stopped by incubating for 3 min at 98°C. The fluorescence microscopy was performed under the same conditions as in the first iteration of this construct.

Growth burden

In order to work with E. coli for designing constructs and testing synthetic biology systems, the growth burden of said synthetic biology tools has to be measured. We performed growth burden evaluation by measuring OD600 for five hours of modified and unmodified E. coli DH5α. The composite of recombinant deacetylase CBD-ProThr box-AnCDA did not inhibit the growth of E. coli as seen in Figure 1.

References

1.Lima, R., Fernandes, C. and Pinto, M.M. (2022) ‘Molecular modifications, biological activities, and applications of chitosan and derivatives: A recent update’, Chirality, 34(9), pp. 1166–1190. doi:10.1002/chir.23477.
2.Torkaman, S. et al. (2021) ‘Modification of chitosan using amino acids for wound healing purposes: A Review’, Carbohydrate Polymers, 258, p. 117675. doi:10.1016/j.carbpol.2021.117675.