Composite

Part:BBa_K5117048

Designed by: Jenny Sauermann, Lilli Kratzer, Katrin Lehmann   Group: iGEM24_TU-Dresden   (2024-09-28)
Revision as of 20:38, 1 October 2024 by Lilli-kratzer (Talk | contribs)


PcotYZ-BsRBS-AtCelO-L2-CotY-B0014

This part serves as transcriptional unit composed of:

  • promoter PcotYZ of Bacillus subtilis (BBa_K5117021)
  • ribosome binding site of Bacillus subtilis (BBa_K5117000)
  • celO gene of Acetivibrio thermocellus without signal peptide encoding an exoglucanase (EC 3.2.1.176),
    • addition of a long flexible linker (L2) downstream of the coding sequence encoding the amino acids (GGGGS)4 (BBa_K5117047)
  • cotY gene of Bacillus subtilis (BBa_K5117022)
  • bidirectional terminator B0014 (BBa_B0014)


Biosafety level: S1

Target organism: Bacillus subtilis

Main purpose of use: Immobilization of AtCelO on the spore crust of B. subtilis (spore surface display)

Application: Degradation of cellulose


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 1184
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 2170
  • 1000
    COMPATIBLE WITH RFC[1000]


Enzyme characterization according to literature

The characterization of the enzyme included in this composite part can be found on the basic part page (BBa_K5117047) of the enzyme.


Construct design

For compatibility with the BioBrick RFC[10] standard, the restriction sites EcoRI, XbaI, SpeI, PstI and NotI were removed from the coding sequence (CDS). To make the part compatible with the Type IIS standard, BsaI and SapI sites were removed as well. This was achieved by codon exchange using the codon usage table of Bacillus subtilis (Codon Usage Database Kazusa).


To express target genes only under sporulation, the sporulation-dependent promoter PcotYZ of B. subtilis was chosen. In previous studies, this promoter has so far provided the highest activity for spore surface display (Bartels et al. 2018, unpublished data of Elif Öztel). The promoter was followed by the ribosome binding site (RBS) for the host B. subtilis with a 7 bp spacer.

To anchor the target enzyme on the spore surface, it was fused to the N-terminus of the anchor protein CotY. This anchor is located in the crust, the outermost spore layer, and has been shown to be well suited for protein immobilization (McKenney et al. 2013, Bartels et al. 2018, Lin et al. 2020).


Moreover, different linkers between the fused target enzyme and anchor protein were analyzed, as these proteins may affect the folding and stability of each other and, eventually, lead to misfolding and reduced activity. Whereas flexible linkers promote the movement of joined proteins and are usually composed of small amino acids (e.g. Gly, Ser, Thr), rigid linkers are usually applied to maintain a fixed distance between the domains (Chen et al. 2013).

Within the framework of the TU Dresden iGEM 2024 Team, three linkers have been tested: 1) A short flexible GA linker (L1) encoding the small amino acids Gly and Ala, 2) A long flexible linker (GGGGS)4 (L2) which is one of the most common flexible linkers consisting of Gly and Ser residues and 3) A rigid linker GGGEAAAKGGG (L3) in which the EAAAK motif results in the formation of an alpha helix providing high stability (Chen et al. 2013).

The composite part documented in this page contains the long flexible linker (GGGGS)4.


Following the CDS of cotY, a spacer consisting of 10 bp of the natural genome sequence downstream from the cotYZ operon was inserted. This creates space before the terminator and ensures that the ribosome is able to read the full length of the CDS. The construct ends with the terminator B0014, a bidirectional terminator consisting of B0012 and B0011.

The entire construct was flanked with the BioBrick prefix and suffix, allowing for cloning via the BioBrick assembly standard and restriction-ligation-cloning. The vector pBS1C from the Bacillus BioBrickBox was used as an integrative plasmid backbone enabling genomic integration into the amyE locus of B. subtilis (Radeck et al. 2013).


Construction of spore display plasmids

First, all biological parts including the enzyme candidate (Fig. 1) as well as the promoter PcotYZ, the terminator B0014 and the anchor gene cotY (Fig. 2) were amplified by PCR and purified using the HiYield® PCR Clean-up/Gel Extraction Kit (SLG, Germany). The RBS was added by oligonucleotides. The plasmid pSB1C3-AtCelO generated in the subcloning phase served as template for PCR of the enzyme candidate (see BBa_K5117015). The linker was added by oligonucleotides. The promoter and anchor gene were amplified from genomic DNA of B. subtilis W168 and the terminator from a plasmid provided by the laboratory collection of Prof. Thorsten Mascher (General Microbiology, TU Dresden).


Fig. 1: Agarose gel electrophoresis: PCR of AtCelO-L2. Oligonucleotides for amplification can be found on the Experiments page. The correct PCR product has a size of 1964 bp. 1 kb Plus DNA Ladder (NEB) served as marker (M). The PCR product was purified by gel extraction resulting in a DNA concentration of 129.1 ng/µl.


Fig. 2: Agarose gel electrophoresis: PCR of PcotYZ, cotY and B0014. Oligonucleotides for amplification can be found on the Experiments page. Amplification of PcotYZ results in a band of 238 bp, L2-cotY displays a band of 544 bp and B0014 140 bp. 1 kb Plus DNA Ladder (NEB) served as marker (M). PCR products were purified resulting in DNA concentrations of 149.1 ng/µl (PcotYZ), 126.9 ng/µl (L2-cotY), and 27.5 ng/µl (B0014).


The composite part was subsequently assembled via Overlap PCR by complementary overhangs, which were designed and added by oligonucleotides (Fig. 3).


Fig. 3: Agarose gel electrophoresis: Overlap PCR of the spore display construct PcotYZ-AtCelO-L2-cotY-B0014. Oligonucleotides for amplification can be found on the Experiments page. The correct PCR product has a size of 2811 bp. Other bands are probably caused by unspecific binding of oligonucleotides. 1 kb Plus DNA Ladder (NEB) served as marker (M). The Overlap PCR product was purified by gel extraction resulting in a DNA concentration of 34.6 ng/µl.


Afterwards, the Overlap PCR product was cloned into the vector backbone pBS1C enabling genome integration into the amyE locus in B. subtilis (Radeck et al. 2013). For that purpose, the insert as well as pBS1C were digested with EcoRI and PstI and purified by PCR clean up (DNA concentration: 26.4 ng/µl and 29.2 ng/µl respectively) using the HiYield® PCR Clean-up/Gel Extraction Kit (SLG, Germany).

After ligation, the plasmid was transformed into chemically competent E. coli DH10β cells and transformants were selected by ampicillin resistance (100 μg/ml ampicillin) encoded on the vector backbone. As the vector was purified via PCR clean up, the vector backbone might re-ligate with the original RFP insert, but colonies with re-ligated plasmids appear pink on the plate and can therefore be distinguished from correct transformants.

The negative control containing no DNA showed no growth. The positive control containing pBS1C resulted in a pink bacterial lawn. The re-ligation control containing the digested vector pBS1C led to growth of approximately 400 pink and 20 white colonies. The transformation with the spore display plasmid pBS1C-PcotYZ-AtCelO-L2-cotY-B0014 resulted in ≈ 300-400 colonies, both pink and white ones.


White colonies transformed with the spore display plasmid were analyzed by Colony PCR and agarose gel electrophoresis (Fig. 4). Colonies with a band at the correct size of the insert were chosen for plasmid isolation according to the HiYield® Plasmid Mini DNA Kit (SLG, Germany). The correct insert sequence of the plasmid was verified via sequencing by Microsynth Seqlab GmbH. Consequently, the spore display plasmid pBS1C-PcotYZ-AtCelOL2-cotY-B0014 was successfully constructed (DNA concentration: 276.9 ng/µl).



Fig. 4: Agarose gel electrophoresis: Insert amplification of PcotYZ-AtCelO-L2-cotY-B0014 by Colony PCR of transformed E. coli DH10β cells. Oligonucleotides for amplification can be found on the Experiments page. Numbers 1-4 correspond to chosen colonies. The correct PCR product has a size of 2872 bp. The negative control displayed no bands. 1 kb Plus DNA Ladder (NEB) served as marker (M). Colony 2 was verified by sequencing and contained the correct insert sequence.


Generation of Bacillus subtilis strains

Ultimately, this plasmid was transformed into the B. subtilis wildtype W168. Transformants were selected by chloramphenicol resistance (5 μg/ml) encoded on the pBS1C vector backbone. The negative control containing no DNA showed no growth. The transformation with the spore display plasmid pBS1C-PcotYZ-AtCelO-L2-cotY-B0014, which was linearized by restriction with BsaI prior to transformation, resulted in ≈ 400-500 white colonies.


The successful genomic integration was verified via starch assay (Fig. 5). Four colonies were transferred onto replica and starch plates. If integration into the amyE locus was successful, the native amylase of Bacillus is not produced correctly, resulting in the organism’s inability to degrade starch. Correct transformants displayed no halo around the cells. The wildtype W168 with a functional amylase was used as a control and produces a clear halo. Two biological duplicates of the engineered B. subtilis strain were chosen for cryo-conservation, with clone 1 being used for subsequent activity tests.



Fig. 5: Starch assay of transformed B. subtilis W168 cells. Numbers 1-4 correspond to chosen colonies. W168 served as control and displayed a bright halo. In contrast, no halo was visible for the W168 strain with the integrated spore display construct.


Spore preparation

Spores were prepared by culturing cells in LB medium with chloramphenicol until they reached the exponential growth phase (OD600 of 0.4–0.6). After washing and resuspension in DSM, the culture was incubated at 37 °C for 24 hours to induce sporulation. The cells were then lysed using lysozyme and washed with dH2O and SDS to remove vegetative cell residues. For qualitative plate assays, an OD600 of 0.2 was used. Further details are available on the Experimentspage.


Detemination of exoglucanase activity with PASC assays and PASA assay

We attempted to determine exoglucanase activity using various methods, including assays with avicel and congo red staining, as well as a cellulose overlay assay. Despite multiple iterations, these approaches were unsuccessful. Ultimately, we established the PASA and PASC assays based on work of Percival Zhang et al. (2006), which allowed for clear visualization of exoglucanase activity through the appearance of clearance zones, as shown in Fig. 6, without the need for additional staining. Details of the assay development can be found on the Engineeringpage.


Fig. 6: PASC and PASA assays for determination of exoglucanase activity. The arrow indicates the zone of clearance, which signifies exoglucanase activity. The sample used was 20 µL of commercially available cellobiohydrolase I, and the plates were incubated at 50 °C for 24 hours.


To examine the functionality of AtCelO-displaying spores (AtCelO-L2), a qualitative assay was performed using PASC-Agar and PASA-Agar plates, following the protocol described on the Experimentspage. Initially, the optical density (OD) of the spore solution was adjusted to 0.2, and 20 µL was pipetted onto the plates. The plates were then incubated at 50 °C for 24 hours, as shown in Figure 7 (example of a PASC assay). However, no activity was detected. Further testing with spore solutions at OD600 ranging from 0.5 to 4.0, as well as incubation at room temperature and 65 °C, also showed no activity (data not shown).


Fig. 7: Qualitative PASC activity assay of AtCelO displaying spores (AtCeO-L2) on PASC-agar plate to examine cellobiohydrolase activity. OD600 of the spore solution was adjusted to 0.2 and 20 µL of the suspension was applied to PASC-agar plates.

References

Bartels J., López Castellanos S., Radeck J., Mascher T. (2018): Sporobeads: The utilization of the Bacillus subtilis endospore crust as a protein display platform. ACS synthetic biology 7(2), 452-461. https://doi.org/10.1021/acssynbio.7b00285

Chen X., Zaro J. L., Shen, W. C. (2013): Fusion protein linkers: property, design and functionality. Advanced drug delivery reviews 65(10), 1357-1369. https://doi.org/10.1016/j.addr.2012.09.039

McKenney P. T., Driks A., Eichenberger P. (2013): The Bacillus subtilis endospore: assembly and functions of the multilayered coat. Nature Reviews Microbiology 11 (1), 33–44. https://doi.org/10.1038/nrmicro2921

Lin P., Yuan H., Du J., Liu K., Liu H., Wang T. (2020): Progress in research and application development of surface display technology using Bacillus subtilis spores. Applied microbiology and biotechnology 104 (6), 2319–2331. https://doi.org/10.1007/s00253-020-10348-x

Öztel, E. & Mascher T. (2024): unpublished data.

Radeck J., Kraft K., Bartels J., Cikovic T., Dürr F., Emenegger J., Kelterborn S., Sauer C., Fritz G., Gebhard S., Mascher T. (2013): The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis. Journal of biological engineering 7, 1-17. https://doi.org/10.1186/1754-1611-7-29

Vellanoweth R. L. & Rabinowitz J. C. (1992): The influence of ribosome‐binding‐site elements on translational efficiency in Bacillus subtilis and Escherichia coli in vivo. Molecular microbiology 6(9), 1105-1114. https://doi.org/10.1111/j.1365-2958.1992.tb01548.x

Percival Zhang, Y. H., Cui, J., Lynd, L. R., & Kuang, L. R. (2006). A transition from cellulose swelling to cellulose dissolution by o-phosphoric acid: Evidence from enzymatic hydrolysis and supramolecular structure. Biomacromolecules, 7(2), 644–648.


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