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Chitin synthase NodC from Rhizobium leguminosarum

The Chitin Synthase (CHS) NodC from Rhizobium leguminosarum is an N-acetylglucosaminyl transferase which catalyzes the formation of chitin pentamers by using UDP-N-acetylglucosamine as donor and N-acetylglucosamine as acceptor.

1. Usage and Biology

Besides cellulose, chitin is the most common natural polysaccharide in nature. Chitin is composed of β(1,4) linked 2-acetamido-2-deoxy-β-D-glucose (N-acetylglucosamine). The polymer is a component of fungi cell walls and the exoskeletons of insects and crustaceans, like crabs or shrimps [Dutta et al., 2004; Kumar, 2000]. The extraction of chitin from crustaceans produces a lot of waste and uses a lot of chemicals. But bacteria, like E. coli can produce chitin via a chitin synthase (CHS) in an environmentally friendly manner. The production of chitin appears to be important as it is a useful substance which finds applications in medicinal, industrial and biotechnological research. Chitin, and its derivate chitosan, is non-toxic, biocompatible and biodegradable. Their bioactivities are for example the promotion of wound healing or hemostatic activity, immune enhancement, eliciting biological responses, and antimicrobial activity [Kurita, 2006]. The nodC gene is originating from the gram-negative bacterium Rhizobium leguminosarum and is a homologue to the chitin synthase from yeast. Rhizobium species live in symbiosis with legumes, where the bacteria form nitrogen-fixing nodules in the legume roots. This interaction leads to an activation of the bacterial nodulation (nod) genes and the secretion of Nod factors. nodC belongs to these nod genes which create and modify the Nod factors. The NodC protein has strongly hydrophobic domains which indicate that it is an integral or transmembrane protein.

2. Mechanism

NodC is involved in the synthesis of chitin oligosaccharides, but only with a polymerization degree up to five [Kamst et al., 1995]. NodC uses UDP-N-acetylglucosamine (UDP-GlcNAc) as sugar donor, which is a precursor for the biosynthesis of peptidoglycan and therefore present in growing bacterial cells. The mechanism of elongation proceeds by a successive inverting nucleophilic substitution reaction at C1 of the UDP-GlcNAc – molecule (Figure 1). UDP departs when the O4 atom of the growing sugar chain attacks as a nucleophile [Dorfmueller et al., 2014]. With a low concentration of UDP-GlcNAc NodC produces a mixture of trimers, tetramers and pentamers and with high concentrations of UDP-GlcNAc it produces pentamers solely. It almost exclusively directs the formation of pentasaccharides [Samain et al., 1997].

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Figure 1: Mechanism of NodC. The enzyme uses UDP-acetylglucosamine as donor and N-acetylglucosamine as acceptor ad creates chitin pentamers.

3. Expression

We ordered the nodC gene via IDT sequencing. We inserted the gene into the pSB1C3 vector via the BioBrick system and verified this via sequencing. One pSB1C3 vector has an AraC promoter system (BBa_K808000) and the other an Anderson Promotor with defined cleavage sites (BBa_K2380025). Both vectors have the RBS BBa_K2380024. Afterwards we transformed the vector in E.coli BL21 for expression studies and started the expression, once by induction with arabinose for the AraC promoter system and the other without induction by the constitutive Anderson promoter. To examine the successful expression, an SDS-PAGE was performed.

4. Purification

The next step was the purification of the protein and the verification of the enzyme function. To purify the enzyme, a site-directed mutagenesis was done at the C-Terminus to add a His-taq and the protein was purified via an EKTA in combination with a 1 mL HisTrap column by GE Healthcare.

5. Activity Assays

5.1 Thin-layer chromatography

Such as every chromatographic method the TLC utilizes the principle of separation based on the different affinity of several compounds inside a mixture towards the stationary planar phase and the mobile phase. That means in detail the compounds run over the stationary phase driven by the capillary effects and under influence of the mobile phase due to their differing affinity. Thereby, small differences in the affinity to the mobile phase are sufficient for getting a clear fractionation. By comparison with a standard, it can be shown that chitin is produced.

5.2 UDP-Glo^TM Glycosyltransferase Assay

NodC is a N-acetylglucosamine transferase that uses UDP-GlcNAc as donor molecule. To test the functionality of the nodC enzyme, the UDP-Glo^TM Glycosyltransferase Assay from Promega was used. The NodC transfers N-acetylglucosamine from the UDP-GlcNAc to single N-acetylglucosamine bricks. The assay is a homogenous, single-reagent-addition method to detect UDP. In a first reaction the glycosyltransferase adds the UDP-GlcNac to the acceptor molecule and UDP is set free. In a second step the UDP is converted to ATP via a UDP Detection Reagent. This ATP generates light in a luciferase reaction which can be measured using a luminometer.

Figure 3: Principle of the UDP-GloTM Glycosyltransferase Assay. After the glycosyltransferase reaction, UDP Detection Reagent is added and UDP is converted to ATP. This converts UDP to ATP and generates light via a luciferase reaction.

Sequence and Features