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 653
Illegal BamHI site found at 580
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

Introduction

pT7-CBDcipA-Pln1

Figure Y. Mechanism of action. The CBDcipA-sfGFP is attached to cellulose. By adding thrombin from any source the fusion protein will be cleaved and sfGFP will be released into the solution. By changing the fusion protein to an antimicrobial peptide/enzyme, and using the cellulose as a bandage, the peptide/enzyme can be released into a wound by native human thrombin.

This part consists of a cellulose binding domain (CBD) from Clostridium thermocellum (C. thermocellum) cellulose scaffolding protein (CipA) and is a central part Clostridium thermocellum's cellusome. The CBD was fused to sfGFP in this part to easily track the binding capacities and to test our release mechanism. The CBD-sfGFP were fused using a flexible GS-linker (-GGGGSGGGGS-). A thrombin cleavage site (-LVPRGS-) was added to the end of the linker and its breakage will leave a glycine and serine attached to the N-terminal of the sfGFP fusion protein.

Assembly compabilities

An internal BamHI recognition sequence (RS) has been added to enable changeable fusion proteins. BamHI was chosen because its RS codes for glycine and serine, fitting it to the end of the thrombin site. It is also cost-effective enzyme and is unaffected by methylated DNA.

This part can be used to track purification, measure CBD binding ability and report cleavage at the thrombin site.

CBDcipA crystal structure

Figure 1. Crystal structure of CBDcipA with a resolution of 1.75 Å which were solved by [http://www.ncbi.nlm.nih.gov/pmc/PMC452321 Tormo et al. 1989]. PDB code 1NBC. In red from the left, W118, R112, D56, H57 and Y67, thought to be the surface which interacts strongly with cellulose.

Important molecular faces

CBDcipA is composed of a nine-stranded beta sandwich with a jelly roll topology and binds a calcium ion. It further contains conserved residues exposed on the surface which map into two clear surfaces on each side of the molecule. One of faces mainly contains planar strips of aromatic and polar residues which may be the cellulose binding part. Further aspect are unknown and unique with this CBD such as the other conserved residues which are contained in a groove.

The choice of cellulose binding domain

iGEM Linköping 2019 choose CBDcipA due to many other iGEM teams exploring the possibilities of this domain. Our basic design was influenced by iGEM14 Imperial, iGEM15 Edinburgh and iGEM18 Ecuador. Purification and where to place the fusion protein (N- or C-terminal) was determined by studying the former projects. CBDcipA also originates from a thermophilic bacteria which further increases the domains applications.

Expression system

The part has a very strong expression with a T7-RNA-polymerase promotor (BBa_I719005) as well as a 5'-UTR (BBa_K1758100) region which has been shown to further increase expression in E. coli (BBa_K1758106), ([http://www.ncbi.nlm.nih.gov/pubmed/2676996 Olins et al. 1989]), ([http://www.ncbi.nlm.nih.gov/pubmed/23927491 Takahashi et al. 2013]). Both this part and the part were sfGFP was changed for AsPink (BBa_K3182000) showed great expression.

Figure B. Benchling screenshot of the expression system. The T7-RNA-polymerase promotor is followed by a T7 g10 leader sequence which enhances the binding to the 16S ribosomal RNA. After the leader sequence a poly A spacer is found, which has been shown to increase translation in vitro. Before the start codon a strong RBS, g10-L, followed by an AT-rich spacer can be seen, which will slightly increase translation of the following gene.

Fusion protein bound to the carbohydrate binding domain

Fused to the CBD is a Lactobacillus plantarum antibacterial peptide. The peptide is 38 amino acids long and has a secondary structure closely resembling membrane proteins. The C-terminal has a high positive charge possibly to find the outer membrane of the target bacteria.

The peptide is designed to battle the Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. family of pathogens (ESKAPE). ESKAPE is a family(ies) of bacteria which has multiple understrains that has evolved resistance to the most commonly used antibiotics.

Usage and Biology

Antimicrobial activity in solution

Figure B. A: CBD-Pln1 2.8 uM was added the E. coli bacterial culture, in the positive control no peptide but the same volume of only water was instead added. B: CBD-Pln1 was bound to cellulose and thrombin was added. Afterwards the supernatant was taken which only contain thrombin, thrombin buffer and the Pln1 peptide. This supernatant was added to an E. coli culture. The positive control contain the thrombin together in thrombin buffer with the same volume as the treatment. C: CBD-Pln1 was bound to cellulose and thrombin was added. Afterwards the supernatant was taken which only contain thrombin, thrombin buffer and the Pln1 peptide. This supernatant was added to a B. subtilis culture. The positive control contain the thrombin together in thrombin buffer with the same volume as the treatment.