Figure 3-1-1 Process of AMP protein purification by nickel columns
Figure 3-1-2 Process of performing SDS-PAGE to verify the AMP protein
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Revision as of 07:36, 4 August 2024
Antimicrobial peptide discoverd from the Lactobacilli in the human vaginal flora Antimicrobial peptide ORF
Contents
Usage and Biology
Antimicrobial peptides (AMP) are a large class of active oligopeptides with antimicrobial properties against harmful life forms (or pathogens) such as bacteria, fungi, parasites and viruses. In addition to their antimicrobial ability, some of these peptides can directly or indirectly participate in the immunomodulation of the host and protect the host from infection. Because they generally have a sufficient amount of positive charge and are often accompanied by hydrophobicity, they can bind to negatively charged biological membranes under electrostatic force, penetrate and destroy the membrane structure to cause cell death. Different from the traditional antibiotic single-target sterilization principle, antimicrobial peptide can carry out multi-target destruction in pathogens, which can greatly reduce the production of drug-resistant bacteria, and has a broad-spectrum antimicrobial properties, which is one of the best choices for replacing antibiotics in the future. In the current global situation, antimicrobial peptides have been used in many clinical treatment cases in bacterial infection, wound healing and cancer treatment. With the development of synthetic biology and biomedical engineering and other interdisciplinary disciplines, the molecular design and biosynthesis of antimicrobial peptides will have more ideas and technical support. Imbalance of intestinal flora and loss of tolerance to local microbiota are possible causes of inducing chronic enteritis. Therefore, regulating the balance of intestinal flora can help alleviate intestinal inflammation and improve the therapeutic effect of chronic enteritis.
We constructed suitable engineered bacterial strains to characterize a novel antimicrobial peptide newly isolated from Lactobacillus from the human vaginal flora in our Host lab (unpublished data). The antimicrobial peptide has been shown to have some bacteriostatic properties after validation with our constructed engineered bacteria. It has a wide range of bacteriostatic activity against Gram-positive and Gram-negative bacteria.
Plasmid construction of a novel antimicrobial peptide AMP
Constitutive plasmid construction
We obtained a novel antimicrobial peptide (AMP) from our host lab, and sent it to the company for gene synthesis to obtain a usable AMP gene sequence. We selected Escherichia coli BL21 (DE3) and strong constitutive promoter J23119 as chassis cell and promoter to enable long-term and efficient antimicrobial peptide expression. On this basis, we will isolate and purify the AMP expressed by our constructed engineered strains and use them as biological agents.
Based on these design principles, we designed plasmid pET29a-pJ23119-RBS-AMP-T7, as shown in Figure 2-1-1. Using homologous recombination integration, expression plasmid pET29a-pJ23119-RBS-AMP-T7 was constructed and transformed into DH5α. We picked several single colonies of E. coli on the transfected plates and then extracted the recombinant plasmid and performed PCR to verify that the primers were specific and the target fragment was 3275 bp, and the results are shown in Figures 2-1-2. We sent the plasmids with the correct positions of the bands to GENEWIZ Co. for sequencing, and the results of the sequencing were correct. The recombinant plasmid pET29a-pJ23119-RBS-AMP-T7 was successfully constructed.
Figure 2-1-1 AMP expression plasmid pET29(a)-pJ23119-RBS-AMP-T
Nitric-Oxide-inducible plasmid construction
Since we changed the therapy from extracting antimicrobial peptides as biological agents for injection to directly taking engineered bacteria for treatment in our project and to validate the part's performance in vitro as much as possible in real treatment scenarios, we optimised and upgraded the engineered bacteria.
We considered the suggestions made by relevant experts and upgraded the engineered bacteria design in two parts, chassis cell and promoter:
- Replacement of chassis cells from BL21 (DE3) to the safe and harmless E. coli Nissle 1917 (EcN)
- Adding the responsive promoter SoxR/SoxS after the strong constitutive promoter J23119
In order to be taken orally, we replaced the chassis cells with EcN, an FDA-approved human probiotic. EcN has been widely used in therapeutic applications and is endotoxin-free, which avoids the problem of endotoxin-containing BL21 (DE3) strains. Adding a responsive promoter ensures that our gene line is turned on and releases antimicrobial peptides in specific enteritis environments, avoiding accidental expression by engineered bacteria. (See ZQT-Nanjing wiki for details)
On these design principles, we designed the plasmid pET29a-pJ23119-SoxR-T-pSoxS-RBS-eGFP-RBS-AMP-T7 as shown in Figure 2-2-1, and using homologous recombination integration, we constructed the expression plasmid pET29a-pJ23119-SoxR-T-pSoxS-RBS-eGFP-RBS-AMP-AMP-T7. We transformed it into DH5α and extracted the recombinant plasmid after picking several single colonies of E. coli on the transformed plates for inoculation. We performed PCR to verify that the primers were specific primers with a target fragment of 4678 bp, and the results are shown in Figures 2-2-2. We sent the plasmids with correct band positions to GENEWIZ Co. for sequencing, and the sequencing results were all correct, which verified that the recombinant plasmid pET29a-pJ23119-SoxR-T-pSoxS-RBS-eGFP-RBS-AMP-T7 was successfully constructed.
Figure 2-2-1 NO-inducible plasmid pET29(a)-pJ23119-SoxR-T-pSoxS-RBS-eGFP-RBS-AMP-T7
Protein expression and purification validation of the novel antimicrobial peptide AMP
SDS-PAGE validation
We extracted the correctly sequenced NO-inducible plasmid and transformed it into EcN for expression. Since NO is hazardous, we utilized SNP (sodium nitroprusside) as a NO donor for inducible expression. SNP can decompose and release NO in the presence of light, thus initiating downstream gene expression.
We picked a single colony, added 5ml LB culture solution in a test tube, added one thousandth (5µl) of the resistance gene Kana, picked the single colony into the test tube, and put it into a 37℃ incubator at 220rpm to incubate for 16 hours. Two tubes of bacteria were raised as experimental group and control group; OD600 of the bacterial solution was measured, and the OD600 of the bacterial solution was diluted to 0.1 (0.1×(50+colonization amount) = OD600×colonization amount), which was added into 250ml conical flasks with 50ml of LB+50µl of Kana, and the culture was amplified for four to five hours, until both flasks of the bacterial solution had an OD600 value close to 1.0. We initially set the induction temperature at 16°C and the induction time at 24 hours, and the final concentration of SNP (sodium nitroprusside) 100µM was replenished every 12 hours. At the end of induction, the protein fragmentation step was carried out, 200 µl of total protein samples from experimental and control groups were dispensed before ultrasonic fragmentation; after fragmentation, 200 µl of supernatant was aspirated as post-fragmentation supernatant, and 200 µl of precipitate was resuspended in ultrapure water as post-fragmentation precipitate. Concentrate by ultrafiltration, take up 200µl of concentrated supernatant as a sample; protein gel sample, 5-10µl for each well site, electrophoresis running gel; Thomas Brilliant Blue medium-high fire staining for two minutes, decolorization.
Because the Marker indication range is 8-200KD, and the AMP size is only 8.5KD after adding His tag, so the bands are not obvious. Therefore, we performed Western Blot protein blotting (WB) to verify whether the protein was expressed.
Western Blot Validation
Through the characterization of the promoter SoxR/SoxS
So we carried out the induction of AMP expression according to the above experimental conditions, picked single colonies, added 5 ml of LB culture medium to the test tube, added one thousandth (5µL) of the resistance gene Kana, picked the single colonies into the test tube, and put them into the 37℃ incubator at 220rpm for 16 hours. Two tubes of bacteria were raised as experimental group and control group. Measure the OD600 of the bacterial solution, dilute the OD600 of the bacterial solution to 0.1 (0.1×(50+colonization amount)=OD600×colonization amount), add it into 250ml conical flasks of 50ml LB+50µl Kana, and amplify the incubation for four to five hours until the OD600 values of both flasks were close to 1.0. Set the induction time to 10 hours, and SNP (sodium nitroprusside) 100µM final concentration was added. Protein fragmentation step was carried out at the end of induction, 200 µl of total protein samples from experimental and control groups were dispensed before ultrasonic fragmentation; after fragmentation, 200µl of supernatant was aspirated as post-fragmentation supernatant sample solution, and 200µl of precipitate was resuspended in ultrapure water as post-fragmentation precipitate. Take 20µl of sample plus 5µl of SDS-PAGE protein sample buffer (5×) cook protein at 100℃ for 10min, protein gel sample, run the gel; run the gel of the rest of the protein sample, transfer the membrane, and do the WB experiment; apply the primary antibody (1:7000) overnight, wash with TBST, apply the secondary antibody (1:5000) for 1hour, continue to wash, and then 1:1 configure the protein developer solution to develop the image.
As can be seen in Figure 3-3 WB development graph, the antimicrobial peptide containing NO-inducible promoter formed inclusion bodies, and the precipitate contained a large amount of AMP, but the induced AMP developed deeper and clearer bands than the background expression level. This indicates that the expression of the antimicrobial peptide mediated by the NO-inducible promoter was successful, and the precipitate contained a large amount of AMP.
Figure 3-2-1 WB characterisation of antimicrobial peptides containing NO-inducible promoter
1-3 are uninduced precipitate, supernatant and total protein, respectively; 4-6 are induced precipitate, supernatant and total protein, respectively; M wells are at Marker 6.5-14.4 KD
Performance testing of the antibacterial effect of the novel antimicrobial peptide AMP
Circle of inhibition test
In order to validate and evaluate the performance of the bacterial inhibition effect of our novel AMP, we will perform the inhibition circle experiment on it.
As shown in Figure 3-4, the antimicrobial peptide had a significant bacteriostatic effect when it was diluted 1000 times. The induced supernatant showed a more significant bacteriostatic effect compared to the control supernatant. It indicates that our novel AMP has a strong performance of bacteriostatic effect.
Figure 4-1-1 Results of the circle of inhibition experiments with antimicrobial peptides
The first row is EcN initial bacteria as indicator bacteria; the second row is EcN-antiAP-1 as indicator bacteria; the third row is EcN-antiAP-1 as indicator bacteria; above the horizontal line is the cell-breakage precipitation; below the horizontal line is the uninduced cell-breakage precipitation; from left to right is the bacterial liquid diluted 100, 1,000, 10,000 times.
Bacterial growth inhibition assay
Sequence and Features
Assembly Compatibility:
- 10COMPATIBLE WITH RFC[10]
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- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 199
- 1000COMPATIBLE WITH RFC[1000]