Difference between revisions of "Part:BBa K4083006"

Revision as of 21:09, 21 October 2021

rhlB with SacI and SalI sites

The rhlB gene is responsible for the production of rhamnosyltransferase called RhlB in Pseudomonas aeruginosa.

Usage and Biology

P. aeruginosa is a gram-negative bacillus and opportunistic pathogen. It secretes rhamnolipids - the rhamnose containing glycolipid biosurfactant. These biosurfactants are used by P. aeruginosa to emulsify the oil substances for easy digestion. Thus, rhamnolipids can increase the availability of fats which can be important in many different areas like petroleum, bioremediation, cosmetics, food, agriculture, etc. [1] However, due to the toxicity and infectiousness of P. aeruginosa, other alternative organisms are tested. Currently, genetically engineered Pseudomonas putida has more promising results than others. P. putida only lacks two enzymes for mono-rhamnolipid production: RhlA and RhlB. These enzymes are encoded by rhlA and rhlB coding regions in rhlAB operon. It was previously thought that rhlA and rhlB forms heterodimer, however, further research showed that they act independently from each other [2].

Our team planned to extract rhLA and rhlB genes from P.aeruginosa and to insert them into pRGPDuo2 plasmid obtained from Gauttam, R. [3] We developed the new approach to increase the P. putida's rhamnolipid synthesis by adding nadE gene which encodes NAD synthetase. This way, we hoped to see more rhamnolipid production in engineered P. putida.

The rhamnosyltransferase B (RhlB) catalyzes the reaction between 3-(3-hydroxyalkanoyloxy)alkanoic acid and dTDP-L-rhamnose which forms mono-rhamnolipid [1].

Figure 1. RhlA and RhlB metabolic pathway

Part functionality

We used our assembled rhlB primers to extract the nadE gene. (https://parts.igem.org/Part:BBa_K4083016, https://parts.igem.org/Part:BBa_K4083018). Obtained genes were amplified in a PCR machine. Then, these PCR products were analyzed in the gel electrophoresis experiment:

Figure 2. Gel electrophoresis of PCR products.

It can be observed that rhlB genes were properly extracted as their bands are located below 1.5kbp which is near the actual size of the nadE gene (1334bp). The smears in each well can result from the high concentration of primers, we learned from our mistake and tried to lower the concentration.

Next, these gels were eluted, and collected genes were inserted into the pRGPDuo2 plasmid. To incorporate nadE genes, we digested plasmids with NheI, SacI, SalI restrictases, and T4 ligase. These plasmids with incorporated nadE gene were electroporated into Pseudomonas putida and Pseudomonas aeruginosa. Unfortunately, due to the lack of time from the COVID-19 situation and late reagents delivery, we were not able to properly insert our genes into P. putida. However, we managed to cultivate P. aeruginosa in kanamycin in LB agar. Then, we extracted these engineered plasmids, and double digested them by SacI and SalI restrictases:

Figure 3. Gel Electrophoresis of extracted plasmids with genes

In this picture, E well contains pRGPDuo2+rhlB which was double digested. The base-pair length corresponds to the actual length of pRGPDuo2 and rhlB.

Analysis of biosurfactnt

Since P. aeruginosa already has rhlB genes, we planned to check to what extent the rhamnolipid production will be increased.

Figure 4. Analysis of emulsification assay results after 24 hours of incubation

A: Treatment with P. aeruginosa Wild type crude biosurfactant (from conventional fermentation) B: Untreated control C: Treatment with P. aeruginosa nadE crude biosurfactant (electrofermentation) D: Treatment with P. aeruginosa rhlA crude biosurfactant (electrofermentation) E: Treatment with P. aeruginosa rhlB crude biosurfactant (electrofermentation) </em>

Table 1. Bioremediation treatment of crude oil contaminated soils with crude biosurfactants from the various production set-ups (electrofermentation) using the different P. aeruginosa strains