Difference between revisions of "Part:BBa K4665005"

Revision as of 17:54, 6 October 2023

Usage and Biology

Biomineralization is the process by which living organisms synthesise minerals (Dhami et al., 2013). Microbial calcium carbonate production can proceed through two main metabolic pathways, using urease or carbonic anhydrase (CA) as the catalysts of the reaction (Chaparro-Acuña et al., 2019). However, synthesis through urea hydrolysis produces toxic byproducts which is not observed in the CA catalyzed pathway.

SazCA, derived from the thermophilic bacterium Sulfurihydrogenibium azorense, is the fastest known carbonic anhydrase to date, boasting a kcat/KM value of 3.5 × 108 M⁻¹ s⁻¹ (De Simone et al, 2015). SazCA facilitates the hydration of carbon dioxide to bicarbonate and protons, creating alkaline conditions that aid the formation of calcium carbonate crystals on the extracellular matrix (EPS) of bacterial cells (Fig. 1) (Anbu, et al., 2016).

To enhance enzymatic efficiency, this composite part expresses the SazCA enzyme as a fusion protein on the cell surface of E. coli. This approach bypasses cellular limitations and directly exposes the enzyme to extracellular CO2, increasing calcium carbonate production on limestone surfaces. This component is based on the findings of Zhu et al. (2022), wherein a membrane fusion protein was designed to showcase SazCA on the surface of E. coli cells. This is achieved by linking the E. coli codon-optimized SazCA enzyme (BBa_K4665120) to the integral membrane protein INPN (BBa_K4665001) using a flexible GGGGS linker (BBa_K2549053).

This composite part consists of three basic parts:

1) Ice nucleation protein N-terminal (INPN): This is the N-terminal of ice nucleation protein which will be embedded into the E. coli cell membrane. The sequence coding for the INPN is preceded by a pelB leader sequence. By attaching the pelB signal peptide in front of the INP protein, the fusion protein will be directed towards the bacterial periplasm where it will be anchored in the cell membrane (Singh et al., 2013). The INPN sequence is followed by two front-end sub-repeat sequences important for the stability of the fusion protein (Zhu et al., 2022). 2) GGGGS linker: The GGGGS flexible linker is composed of a sequence of 4 glycine repeats followed by a serine amino acid. This flexible linker is used to connect the N-terminal of the INP to the carbonic anhydrase. 3) SazCA: This sequence codes for the carbonic anhydrase derived from Sulfurihydrogenibium azorense (SazCA). This sequence has been codon optimised for E. coli. The SazCA coding sequence is followed by a His-tag which facilitates the purification and detection of the fusion protein.

Figure taken from Zhu et al., (2021).

Characterisation

Expression:

After successful transformation into BL21 DE3 E. coli, the expression of our recombinant protein was tested. The construct is preceded by the T7 promoter, therefore expression of recombinant protein can be induced through addition of Isopropyl β-D-1-thiogalactopyranoside (IPTG). Liquid overnight cultures of the transformed E. coli were induced with IPTG and samples were taken at different incubation times. Membrane protein extraction was performed by incubation with NPI-10 buffer followed by sonication. SDS PAGE and western blot was performed with antibodies that bind to the 6X-His tag attached at the end of the fusion protein. Previous iterations of the Western Blot revealed the problem of a leaky T7 promoter in our recombinant plasmid, leading to protein expression in absence of IPTG. Previous research has shown that addition of glucose to BL21 DE3 bacterial culture can reduce the background expression of the uninduced gene (Pan & Malcolm, 2000). In our Western Blot we tested various controls, the transformed BL21 DE3 cultures induced with IPTG at different time intervals and the transformed BL21 DE3 cultures that were grown overnight in the presence of glucose.

Gel 1:

Gel 2:

The results show that addition of 0.5% or 1% glucose leads to reduced expression of the recombinant protein in the uninduced samples compared to uninduced culture lacking glucose. Our recombinant protein was most abundant in the transformed BL21 DE3 culture that had been induced with IPTG for 2 hours. In Vitro Mineralization: To test the ability of engineered BL21(DE3) E. coli strain to precipitate CaCO₃, we performed an in vitro mineralisation assay, adapting Zhu, et al. 's technique. Bacteria were cultured overnight in 30mL of LB +Kanamycin medium and 0.5 mM ZnSO₄ at 25℃. IPTG induction was performed 3 hours prior to experimentation. The assay was run on 8 mL Tris-HCl buffer 8.3 and 50mL of saturated CO2 aqueous solution at 0℃. 3 mL of cell pellet were introduced into the solution, and the reaction was allowed to proceed on ice for an hour. At this point, the bacteria should have been able to produce bicarbonate ions. Cells were removed from the solution by centrifugation (15 min x 5000g). 25mL of a 0.3M solution of CaCl₂ was added to the remaining supernatant as a calcium source. The reaction was left to run at 25℃ for 12h. Samples were filtered using vacuum filtration and dried at 50℃ to evaporate the solvent. Solid mass was weighed and recorded as “Wet Weight”. Upon preliminary analysis of FT-IR data, it was concluded that the mineral sample contained a large amount of water, elucidated by the stretching O-H peak at 3400 cm.1. Hence, the sample was dried further in liquid nitrogen for 48 hours, final weight was recorded at 2.3 g (yield=306.17%). Precipitated dry crystals were analysed using ATR-IR and 13C NMR. Enzymatic activity of SazCA: To measure the activity of the SazCA construct, a colorimetric Wilbur Anderson assay was adapted from Kim & Jo, (2022). The assay measures the ability of carbonic anhydrase to hydrate CO₂. Protons released during the hydration reaction cause a decrease in the pH of the solution. Such displacement of H⁺ can be recorded as a function of time taken for pH to shift from 8.5 to 6.5. The colorimetric approach taken for the assay indirectly measured the change of pH by recording the colour change of phenol red upon the addition of SazCA. A reaction buffer of 20mM Tris pH. 8.3 (pKa=8.1) and 100µM phenol red (pKa=7.9) was used. Phenol red was chosen as the pH indicator as it shifts colours from yellow to pink over a pH range of 6.3 to 8.3. Total reaction volume was 1mL. 10µL of SazCA-BL21(DE3) culture were added into a cuvette for each reaction. Varying amounts of saturated CO2 aqueous solution (0.279M) were added, volume filled to 1mL with corresponding amounts of reaction buffer. Data collection was performed by UV-Vis spectrophotometry, measuring absorbance change at 570 nm using the kinetics function of the spectrophotometer, recording every 0.1s for 30 minutes. All reactions were performed ice-cold. The blank reaction consisted of 600µL reaction buffer and 400µL CO2 solution. SazCA samples compared to WT BL21. Abs values were obtained as a colorimetric reference for the reaction buffer adjusted for pH at 8.3, 7.5, and 6.5. Wilbur-Anderson Units (WAU) were calculated according to the following formula: WAU=(t0-t)/t, where t0 is the time (s) taken for the control to undergo a colour shift, and t is the time taken for SazCA samples to undergo a colour shift. ===References=== Anbu, P. et al. (March 1, 2016). Formations of calcium carbonate minerals by bacteria and its multiple applications. Springerplus 5(250). https://doi.org/10.1186/s40064-016-1869-2 Chaparro-Acuña, S.P., et al. (June, 2018). Soil bacteria that precipitate calcium carbonate: mechanism and applications of the process. Acta Agronómica 67(2). https://doi.org/10.15446/acag.v67n2.66109 De Luca, V. et al. (March 15, 2013). An α-carbonic anhydrase from the thermophilic bacterium Sulphurihydrogenibium azorense is the fastest enzyme known for the CO2 hydration reaction. Bioorganic & Medicinal Chemistry Letters, 21(6): 1465.1469. https://doi.org/10.1016/j.bmc.2012.09.047 De Simone, G., et al. (May 1, 2015). Crystal structure of the most catalytically effective carbonic anhydrase enzyme known, SazCA from the thermophilic bacterium Sulfurihydrogenibium azorense. Bioorganic & Medicinal Chemistry Letters, 1;25(9): 2002-2006. https://doi.org/10.1016/j.bmcl.2015.02.068 Dhami, N.K., et al. ( May 2013). Biomineralization of calcium carbonate polymorphs by the bacterial strains isolated from calcareous sites. Journal of Microbiology and Biotechnology, 23(5): 707-714. https://doi.org/10.4014/jmb.1212.11087 Jo, B.H. (October 3, 2013). Engineered Escherichia coli with Periplasmic Carbonic Anhydrase as a Biocatalyst for CO2 Sequestration. Applied and Environmental Microbiology. https://doi.org/10.1128/AEM.02400-13 Kim, J. H., & Jo, B. H. (2022). A Colorimetric CO2 Hydration Assay for Facile, Accurate, and Precise Determination of Carbonic Anhydrase Activity. Catalysts, 12(11), 1391. MDPI AG. http://dx.doi.org/10.3390/catal12111391 Pan, S. H., & Malcolm, B. A. (2000). Reduced background expression and improved plasmid stability with pET vectors in BL21 (DE3). BioTechniques, 29(6), 1234–1238. https://doi.org/10.2144/00296st03 Zhu, Y., et.al (December 6, 2021). Surface display of carbonic anhydrase on Escherichia coli for CO2 capture and mineralisation. Synthetic and Systems biotechnology, 7(1): 460-473. https://doi.org/10.1016%2Fj.synbio.2021.11.008 Sequence and Features BBa_K4665005 SequenceAndFeatures

@@ Line 13: / Line 13: @@
           padding: 10px;
           box-sizing: border-box;
+      }
+     .img-text-container{
+      display: flex;
+      flex-direction: row;
+      }
+     .text-box{
+      padding: 10px;
        }
      </style>
    </head>
    <body>
+    <div class="img-text-container">
      <div class="image-box">
-       <img class="custom-img" height="250px" width="350px" src="https://static.igem.wiki/teams/4665/wiki/parts-registration-images/bba-k4665005-sazca-reaction.jpg" alt="Image 1">
+       <img height="250px" width="350px" src="https://static.igem.wiki/teams/4665/wiki/parts-registration-images/bba-k4665005-sazca-reaction.jpg" alt="Image 1">
 </img>
      </div>
+    <div class="text-box">
 To enhance enzymatic efficiency, this composite part expresses the SazCA enzyme as a fusion protein on the cell surface of <i>E. coli</i>. This approach bypasses cellular limitations and directly exposes the enzyme to extracellular CO2, increasing calcium carbonate production on limestone surfaces.
 This component is based on the findings of Zhu et al. (2022), wherein a membrane fusion protein was designed to showcase SazCA on the surface of <i>E. coli</i> cells. This is achieved by linking the <i>E. coli</i> codon-optimized SazCA enzyme (<b>BBa_K4665120</b>) to the integral membrane protein INPN (<b>BBa_K4665001</b>) using a flexible GGGGS linker (<b>BBa_K2549053</b>).
+  </div>
+  </div>
    </body>
 </html>
@@ Line 30: / Line 40: @@
 <b>This composite part consists of three basic parts:</b>
+<html>
+  <body>
+    <div class="img-text-container">
+    <div class="text-box">
 ) Ice nucleation protein N-terminal (INPN): This is the N-terminal of ice nucleation protein which will be embedded into the <i>E. coli</i> cell membrane. The sequence coding for the INPN is preceded by a pelB leader sequence. By attaching the pelB signal peptide in front of the INP protein, the fusion protein will be directed towards the bacterial periplasm where it will be anchored in the cell membrane (Singh et al., 2013). The INPN sequence is followed by two front-end sub-repeat sequences important for the stability of the fusion protein (Zhu et al., 2022).
@@ Line 36: / Line 49: @@
 ) SazCA: This sequence codes for the carbonic anhydrase derived from Sulfurihydrogenibium azorense (SazCA). This sequence has been codon optimised for <i>E. coli</i>. The SazCA coding sequence is followed by a His-tag which facilitates the purification and detection of the fusion protein.
-<html>
+    </div>
-  <body>
      <div class="image-box">
        <img height="400px" width="500px" src="https://static.igem.wiki/teams/4665/wiki/surface-display-sazca.png" alt="Image 1">
+    </div>
      </div>
    </body>