Difference between revisions of "Part:BBa K5117012"

Revision as of 08:18, 30 September 2024

BsRBS-BpEglA

This part serves as translational unit composed of the ribosome binding site of Bacillus subtilis (BBa_K5117000) and the eglA gene of Bacillus pumilus (BBa_K5117002) encoding an endoglucanase (EC 3.2.1.4).

Target organism: Bacillus subtilis

Main purpose of use: Testing enzyme functionality in the host Bacillus subtilis

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 419
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
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_K5117002) of the enzyme.

Construct Design

For compatibility with the BioBrick RFC[10] standard, the restriction sitesEcoRI, 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). Upstream from the CDS, there is the ribosome binding site (RBS) for the host Bacillus subtilis followed by a 7 bp spacer. This composite part composed of RBS and CDS was flanked by the BioBrick prefix and suffix sequences and ordered via gene synthesis from IDT.

Construction of a template plasmid

In order to create a template from which this part could be amplified, the part was subcloned into a small vector pSB1C3 (Part:pSB1C3). For that purpose, the plasmid was isolated from E. coli DH10β yielding a DNA concentration of 431.0 ng/µl. Afterwards, a Backbone PCR with pSB1C3 (Fig. 1) was performed, followed by a restriction digest of the amplified vector backbone and the parts with EcoRI and PstI, which were purified via the HiYield® PCR Clean-up/Gel Extraction Kit (SLG, Germany), resulting in DNA concentrations of 32.6 ng/µl (digested pSB1C3) and 17.2 ng/µl.

Fig. 1: DNA Ladder (A) and agarose gel electrophoresis of pSB1C3 Backbone PCR (B). A: 1 kb Plus DNA Ladder from New England Biolabs (NEB). B: Backbone PCR of pSB1C3. Oligonucleotides for amplification can be found on the Experiments page. The correct PCR product has a size of 2043 bp. DNA fragments of other sizes represent unspecific bands. 1 kb Plus DNA Ladder (NEB) served as marker (M). The pSB1C3 backbone was purified by gel extraction resulting in a DNA concentration of 190.2 ng/µl.

After ligation, the plasmid was transformed into chemically competent E. coli DH10β cells. Transformants were selected by chloramphenicol resistance (35 µg/ml chloramphenicol) encoded on the pSB1C3 backbone. For the negative control, no DNA was added during the transformation procedure leading to no colony growth on selection plates. For the positive control, cells were transformed with the vector pSB1C3 resulting in a pink bacterial lawn due to the original RFP insert. On the selection plates of the target construct, white colonies were tested for the presence of the correct insert by Colony PCR and agarose gel electrophoresis (Fig. 2).

Fig. 2: Agarose gel electrophoresis: Insert amplification of pSB1C3-BpEglA 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 2309 bp. The negative control displayed no band. 1 kb Plus DNA Ladder (NEB) served as marker (M). Colony 2 resulted in the highest plasmid concentration and was subsequently verified by sequencing revealing the correct insert sequence.

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). Finally, the plasmid was verified via sequencing by Microsynth Seqlab GmbH (DNA concentration: 233.3 ng/µl).

Cloning into inducible expression vectors

For testing the functionality and activity of this enzyme, the part was cloned into xylose-inducible expression vectors in order to overexpress the gene of interest. Replicative (pBS0E-xylR-P_xylA) and integrative (pBS2E-xylR-P_xylA) vectors were used, both with a xylose-inducible promoter for induced expression and a xylose repressor to decrease basal promoter activity (Popp et al. 2017). Whereas replicative plasmids provide a high copy number and result in high concentrations of target proteins, genomic integration (in this case into the lacA locus) ensures high stability but results in lower protein concentrations. The vectors were isolated from E. coli DH10β, resulting in DNA concentrations of 151.9 ng/µl pBS0E-xylR-P_xylA and 127.6 ng/µl pBS2E-xylR-P_xylA. These vectors were digested with EcoRI and PstI (Fig. 3) and purified via gel extraction using the HiYield® PCR Clean-up/Gel Extraction Kit (SLG, Germany).

Fig. 3: Agarose gel electrophoresis: Restriction (Res) of expression vectors pBS0E-xylR-P_xylA (pBS0EX) and pBS2E-xylR-P_xylA (pBS2EX) with EcoRI and PstI. The digested plasmid backbones have sizes of 8114 bp and 7758 bp, respectively. Strong bands at approximately 9000 bp could represent undigested plasmids as well as digested ones due to high size inaccuracy of large bands. Weak bands at 1102 bp represent the RFP insert being cut out of the vector. Large bands were purified by gel extraction and resulted in 17.9 ng/µl and 31.3 ng/µl DNA for the digested vectors pBS0EX and pBS2EX, respectively. 1 kb Plus DNA Ladder (NEB) served as marker (M).

The enzyme part was amplified via PCR (Fig. 4) using the plasmid template pSB1C3-BpEglA and subsequently digested and purified via PCR clean up.

Fig. 4: Agarose gel electrophoresis: PCR of part BpEglA. Oligonucleotides for amplification can be found on the Experiments page. The correct PCR product has a size of 2046 bp. The larger band probably represents the plasmid pSB1C3-BpEglA used as template. 1 kb Plus DNA Ladder (NEB) served as marker (M). BpEglA was purified by gel extraction resulting in a DNA concentration of 138.2 ng/µl.

After ligation, the plasmids were transformed into chemically competent E. coli DH10β and transformants were selected by ampicillin resistance (100 µg/ml ampicillin) encoded on the vector backbone. White colonies transformed with the expression plasmids were analyzed by Colony PCR and agarose gel electrophoresis (Fig. 5). Colonies with a band the correct size of the insert were chosen for plasmid isolation. Finally, the replicative expression plasmid pBS0E-xylR-P_xylA-BpEglA and the integrative expression plasmid pBS2E-xylR-P_xylA-BpEglA were verified by sequencing and successfully generated (DNA concentrations: 427.9 ng/µl, 138.1 ng/µl).

Fig. 5: Agarose gel electrophoresis: Insert amplification of pBS0E-xylR-P_xylA-BpEglA (pBS0EX-BpEglA) and pBS2E-xylR-P_xylA-BpEglA (pBS2EX-BpEglA) by Colony PCR of transformed E. coli DH10β cells. Oligonucleotides for amplification can be found on the Experiments page. Numbers 1-8 correspond to chosen colonies. Correct PCR products have a size of 2197 bp for pBS0EX-BpEglA and 2398 bp for pBS2EX-BpEglA. Negative controls (NC) displayed no band. NCs were loaded onto another gel and are therefore not depicted. 1 kb Plus DNA Ladder (NEB) served as marker (M). Colony 7 of pBS0EX-BpEglA and colony 2 of pBS2EX-BpEglA were verified by sequencing and contained the correct insert sequence.

Ultimately, these expression plasmids were transformed into the target host B. subtilis. Since this part was included in the strategy focused on the secretory expression of target enzymes, WB800N was chosen as an expression strain. This genetically engineered variant of B. subtilis W168 features the disruption of all extracellular proteases. The eight-extracellular-protease-deficient mutant is widely used in industrial applications, as it increases the stability of secreted proteins (Jeong et al. 2018). The transformants were selected by MLS resistance (1 micro;g/ml erythromycin and 25 micro;g/ml lincomycin) encoded on the vector backbones. The Bacillus transformation was carried out with early addition of DNA to growing WB800N cells (at OD₆₀₀ ≈ 0.7) to not miss the timepoint of competence. Afterwards, cells were grown until OD₆₀₀ ≈ 1.1-1.3 and the same procedure was followed as in the initial protocol (see Experiments page). The expression plasmids could be transformed into WB800N and colonies were verified by Colony PCR. The presence of replicative plasmids was tested by two primer pairs (double check), whereas both upstream and downstream integration into the lacA locus was checked for integrative plasmids (Fig. 6). Two colonies each with the correct insert size were chosen for cryo-conservation, serving as biological duplicates.

Fig. 6: Agarose gel electrophoresis: Insert amplification of pBS0E-xylR-P_xylA-BpEglA (pBS0EX-BpEglA) and pBS2E-xylR-P_xylA-BpEglA (pBS2EX-BpEglA) by Colony PCR of transformed B. subtilis WB800N cells. Oligonucleotides for amplification can be found on the Experiments page. Numbers 1-4 correspond to chosen colonies. 1 kb Plus DNA Ladder (NEB) served as marker (M). pBS0EX: Primer pair 1 was used for the amplification of a small fragment including BpEglA only (2046 bp). Primer pair 2 was used for amplification of a large fragment including xylR-P_xylA-BpEglA (3677 bp). Colonies 1 and 3 of pBS0EX-BpEglA were correct and chosen for cryo-conservation. pBS2EX: Primer pair 3 was used to check downstream integration by amplification of a fragment including BpEglA and ‘lacA (2584 bp). Primer pair 4 was used to check upstream integration by amplification of a fragment including lacA’ and the erythromycin resistance gene erm (1370 bp).Colonies 2 and 3 of pBS2EX-BpEglA were correct and chosen for cryo-conservation. Negative controls of all primer pairs (NC 1-4) displayed no bands.

References

Jeong H., Jeong D. E., Park S. H., Kim S. J., Choi S. K. (2018): Complete Genome Sequence of Bacillus subtilis Strain WB800N, an Extracellular Protease-Deficient Derivative of Strain 168. Microbiol Resour Announc. 7(18), e01380-18. https://doi.org/10.1128/MRA.01380-18

Popp P. F., Dotzler M., Radeck J., Bartels J., Mascher T. (2017): The Bacillus BioBrick Box 2.0: expanding the genetic toolbox for the standardized work with Bacillus subtilis. Scientific reports 7(1), 15058. https://doi.org/10.1038/s41598-017-15107-z

@@ Line 53: / Line 53: @@
 Whereas replicative plasmids provide a high copy number and result in high concentrations of target proteins, genomic integration (in this case into the <i>lacA</i> locus) ensures high stability but results in lower protein concentrations.
 The vectors were isolated from <i>E. coli</i> DH10β, resulting in DNA concentrations of 151.9 ng/&micro;l pBS0E-<i>xylR</i>-P<sub><i>xylA</i></sub> and 127.6 ng/&micro;l pBS2E-<i>xylR</i>-P<sub><i>xylA</i></sub>. These vectors were digested with <i>Eco</i>RI and <i>Pst</i>I (Fig. 3) and purified via gel extraction using the HiYield® PCR Clean-up/Gel Extraction Kit (SLG, Germany). </p>
@@ Line 71: / Line 70: @@
 After ligation, the plasmids were transformed into chemically competent <i>E. coli</i> DH10β and transformants were selected by ampicillin resistance (100 &micro;g/ml ampicillin) encoded on the vector backbone.
 White colonies transformed with the expression plasmids were analyzed by Colony PCR and agarose gel electrophoresis (Fig. 5). Colonies with a band the correct size of the insert were chosen for plasmid isolation. Finally, the replicative expression plasmid pBS0E-<i>xylR</i>-P<sub><i>xylA</i></sub>-BpEglA and the integrative expression plasmid pBS2E-<i>xylR</i>-P<sub><i>xylA</i></sub>-BpEglA were verified by sequencing and successfully generated (DNA concentrations: 427.9 ng/&micro;l, 138.1 ng/&micro;l).
@@ Line 110: / Line 108: @@
 Ultimately, these expression plasmids were transformed into the target host <i>B. subtilis</i>. Since this part was included in the strategy focused on the secretory expression of target enzymes, WB800N was chosen as an expression strain. This genetically engineered variant of <i>B. subtilis</i> W168 features the disruption of all extracellular proteases. The eight-extracellular-protease-deficient mutant is widely used in industrial applications, as it increases the stability of secreted proteins (Jeong <i>et al.</i> 2018).
 The transformants were selected by MLS resistance (1 micro;g/ml erythromycin and 25 micro;g/ml lincomycin) encoded on the vector backbones.
-The <i>Bacillus</i> transformation was carried out with early addition of DNA to growing WB800N cells (at OD<sub>600</sub> ≈ 0.7) to not miss the timepoint of competence. Afterwards, cells were grown until OD<sub>600</sub> ≈ 1.1-1.3 and the same procedure was followed as in the initial protocol (see <html><a href=„https://2024.igem.wiki/tu-dresden/experiments">Experiments</a></html> page).
+The <i>Bacillus</i> transformation was carried out with early addition of DNA to growing WB800N cells (at OD<sub>600</sub> ≈ 0.7) to not miss the timepoint of competence. Afterwards, cells were grown until OD<sub>600</sub> ≈ 1.1-1.3 and the same procedure was followed as in the initial protocol (see <html><a href="https://2024.igem.wiki/tu-dresden/experiments">Experiments</a></html> page).
 The expression plasmids could be transformed into WB800N and colonies were verified by Colony PCR. The presence of replicative plasmids was tested by two primer pairs (double check), whereas both upstream and downstream integration into the <i>lacA</i> locus was checked for integrative plasmids (Fig. 6). Two colonies each with the correct insert size were chosen for cryo-conservation, serving as biological duplicates.