Golden Gate Assembly: Prefix/Suffix Block

For efficient golden gate assembly, our team prepared a gene fragment that only contains BsaI sequences and its cleavage site so that the prefix and suffix could be flexibly changed and attached to both ends of the transcription unit, assembled using SapI. The advantage of this method is that it is possible to greatly increase the number of gene fragments that can be synthesized using the golden gate assembly at once without the need to use various plasmids by ordering a prefix/suffix fragment at a low price. According to NEB, it was confirmed that their high-fidelity restriction enzyme could synthesize up to 52 gene fragments at a time. The first BsaI prefix and the last BsaI suffix have EcoRI and BamHI cleavage sites for double digestion and ligation to pCambia 2300 vector for agrobacterium-mediated microalgae transformation.


[Figure 1] BsaI Prefix/Suffix

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[Figure 2] Simple Diagram of level 1~3 assembly

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General Description

Our team has designed and tested various biosensors for C. vulgaris, using inducible promoters and recombinases. Inducible promoters are triggered only at certain conditions, working as biosensors. Our team has further developed the inducible promoters into bio-switch by utilizing recombinases, thereby creating C. vulgaris strain that can constantly express certain genes once the switch is turned on. The detailed structure of the biosensors and switches is described below.

In this project, two types of inducible promoters, pHsp70A (Kropat et al., 1995), pCnAFP (Kim et al., 2020), two types of recombinases, phiC31 (Thomson et al., 2010) and Cre (Sauer & Henderson, 1988), and a quorum sensing system, pTra(4X)::m35S (You et al., 2006), are tested in C. vulgaris. The expression of these bio-bricks has been tested in eukaryotic cells but has not been tested specifically for C. vulgaris. The purpose of this project is to validate the expression of these bio-bricks for C. vulgaris and to utilize them for the development of efficient biosensors and switches.

Our research and development will not stop at biosensors and bio-switches. We designed a bio-switch using an inducible promoter and recombinase, and also designed a quorum sensing system for microalgae. Using these biosensors together, replacing GFP with toxin or antitoxin, our team’s final goal is to develop an effective biocontainment system for genetically modified microalgae-bacteria consortia that can be used in wastewater treatment systems.




Detailed Description for Each Biosensors

Biosensor #1: Inducible Promoters (pHSP70A)

In this project, two types of inducible promoters, pHsp70A (Kropat et al., 1995), pCnAFP (Kim et al., 2020), two types of recombinases, phiC31 (Thomson et al., 2010) and Cre (Sauer & Henderson, 1988), and a quorum sensing system, pTra(4X)::m35S (You et al., 2006), are tested in C. vulgaris. The expression of these bio-bricks has been tested in eukaryotic cells but has not been tested specifically for C. vulgaris. The purpose of this project is to validate the expression of these bio-bricks for C. vulgaris and to utilize them for the development of efficient biosensors and switches.

Our research and development will not stop at biosensors and bio-switches. We designed a bio-switch using an inducible promoter and recombinase, and also designed a quorum sensing system for microalgae. Using these biosensors together, replacing GFP with toxin or antitoxin, our team’s final goal is to develop an effective biocontainment system for genetically modified microalgae-bacteria consortia that can be used in wastewater treatment systems.


Biosensor #1-2: Cold-inducible Promoter (pCnAFP)

pCnAFP is a cold-inducible promoter derived from a polar diatom, Chaetoceros neogracile. The transcription initiation of a cold inducible promoter is activated when cells are exposed to low temperature, 10 °C for 2 hours (Kim et al., 2020).


Biosensor #2: Bioswitch: Inducible Promoter - Recombinase Activity

The bio-switch functions by activating inducible promoters to trigger recombinases, which can irreversibly convert the genetic sequence. With site-specific recombinases, phiC31 and Cre, precise DNA cleavage and ligation are possible. Site-specific recombinases efficiently catalyze recombination between specific targeting sites to delete, insert, invert, or exchange DNA. Therefore, these groups of enzymes are capable of site-specific deletions, excising unwanted DNA from the genome (Thomson et al., 2010).

The Streptomyces phage PhiC31 can site-specifically integrate DNA into the bacterial host by integrating a pair of specific recognition sites attP and attB (attachment site Phage/attachment site Bacteria) (Thomson et al., 2010).

>A 38-kDa Cre protein, from coliphage P1, can promote genetic synapsis and DNA recombination in eukaryotic cells. The recombination takes place at a specific location known as lox. The recombination between two lox sites, similar to that of phiC31 recombinase, can only be catalyzed by Cre recombinase (Sauer & Henderson, 1988).

In this regard, the sequence between two attachment sites can be irreversibly deleted from the genome. This way, it is possible to start or stop the transcription of certain genes when needed, using an inducible promoter and recombinase, as shown below.


Biosensor #3: Quorum-Sensing Promoter & Protein (Tra(4X)::m35S & VP16 TAD::TraR)

The quorum-sensing system of bacteria is tested in microalgae. In the case of the quorum-sensing activator, TraR, corresponding to the quorum-sensing-controlled promoter, pTraR, it is fused with the VP16 protein to increase the reactivity in eukaryotic cells (You et al., 2006). The quorum sensing-controlled promoter is activated only when there is AHL produced in the presence of a bacterial signal molecule called N-3-oxo-octanoyl homoserine lactone (C8 AHL).

In this experiment, the quorum sensing promoter (Tra(4X) :: m35S) and the quorum sensing protein (VP16 TAD :: TraR) are tested in C. vulgaris because their effects in plant cells were verified. The Bacterial quorum sensing promoter and protein were used after slight modification in a way such that they could be expressed and operated in eukaryotic cells. In the case of Tra Promoter, when TraR protein binds to C8AHL, it attaches to the Tra box (5′-ATGTGCAGATCTGCACAT-3′) and induces the operation of bacterial Tra-quorum-sensing-controlled promoter (pTraR). Therefore, the part from pTraR that functions as the binding site for TraR protein are combined with the promoter for plant cells. For the plant cell promoter, minimal CAMV 35S promoter (m35S) is used.

The bacterial quorum sensing protein, TraR, is also modified. C8 AHL function as an inducer, and TraR is its receptor/regulator. The C-terminal region of the TraR protein is responsible for the transcriptional activation and binding to the Tra box of pTraR. For its operation in eukaryotic cells, the TraR is C-terminally fused with the transactivation domain of Virus Protein 16 (VP16 TAD), derived from Herpes simplex virus-1 (You et al., 2006). VP16 functions for viral gene transcription and replication, promoting its expression after infection (Reyes et al., 2022). In this regard, fusing VP16 TAD to TraR can increase the reactivity of the quorum sensing in a eukaryotic cell.



Experiment Design

Biosensor #1: Heat shock-inducible Promoter

Heat shock-inducible promoter activity in C. vulgaris is tested by observing GFP expression. The fluorescence intensity was compared with control.

  • pHsp70A > Kozak > egfp > Tnos
      a. Incubation in the dark and shifted into the light for 1 h.
      b. Incubation in the light and exposed to heat shock (40°C) for 30 min.
    p35S > Kozak > eGFP > Tnos (Control)



  • Biosensor #1-2: Cold-inducible Promoter

    Cold-inducible promoter activity in C. vulgaris is tested by observing GFP expression. The fluorescence intensity was compared with control.

  • pCnAFP>Kozak>eGFP>Tnos
      a. Incubation in low temperature (10°C) for 2 hour.
    p35S>Kozak>eGFP>Tnos (Control)



  • Biosensor #2: Bioswitch: Inducible Promoter - Recombinase Activity

    Recombinase activity, triggered by inducible promoters, is tested by observing GFP expression. The fluorescence intensity was compared with control.

    p35S>attB>mCherry>Tnos : pHSP70A>Kozak>phiC31>Tnos : attP>Kozak>eGFP>Tnos
    (Heat shock inducible promoter + phiC31 recombinase)
    • - After recombination : p35S > attB-attP > Kozak > eGFP > Tnos
      a. Incubation in the dark and shifted into the light for 1 h.
      b. Incubation in the light and exposed to heat shock (40°C) for 30 min.


    p35S>attB>mCherry>Tnos : pCnAFP>Kozak>phiC31>Tnos : attP>Kozak>eGFP>Tnos
    (Cold inducible promoter + phiC31 recombinase)
      - After recombination : p35S > attB-attP > Kozak > eGFP > Tnos
      a. Incubation in low temperature (10°C) for 2 hours.


    p35S>loxP(1)>mCherry>Tnos : pHSP70A>Kozak>Cre>Tnos : loxP(2)>Kozak>eGFP>Tnos
    (Heat shock inducible promoter + Cre recombinase)
      - After recombination : p35S > loxP(1)-loxP(2) > Kozak > eGFP > Tnos
      a. Incubation in the dark and shifted into the light for 1 h.
      b. Incubation in the light and exposed to heat shock (40°C) for 30 min.


    p35S>loxP(1)>mCherry>Tnos : pCnAFP>Kozak>Cre>Tnos : loxP(2)>Kozak>eGFP>Tnos
    (Cold inducible promoter + Cre recombinase)
      - After recombination : p35S > loxP(1)-loxP(2) > Kozak > eGFP > Tnos
      a. Incubation in low temperature (10°C) for 2 hours.
    p35S>eGFP>nos terminator (Control)



  • Biosensor #3: Quorum-Sensing Promoter & Protein

    Quorum-Sensing promoter activity in C. vulgaris is tested by observing GFP expression. The expression is observed in various concentrations of N-3-oxo-octanoyl homoserine lactone (C8 AHL). The observation is made in liquid medium with 0 μM, 0.1 μM, 1 μM, 100μM, 1000 μM, 10000 μM C8 AHL. The fluorescence intensity was compared with control.

    p4X(TraR)::m35S>Kozak>eGFP>Tnos : pHSP70A/pRbcS2>Kozak>VP16 TAD::TraR>Tnos
    p4X(TraR)::m35S>Kozak>eGFP>Tnos : p35S>Kozak>VP16 TAD::TraR>Tnos
    p35S>Kozak>eGFP>Tnos (Control)



    Experiment Protocol

    Microalgae Transformation (Cha et al., 2012)

    1. The mediums and supplements for microalgae transformation are obtained from Kisan Bio, South Korea.
    1. 1. Supplement Luria Broth with 5 mM glucose, 50 mg/L kanamycin
    2. 2. Inoculate Agrobacterium. Tumefaciens (KCTC 12031) single colonies in 10mL of Luria Broth
    3. 3. Under constant agitation at 200 rpm on a rotary shaker at 30°C, culture overnight in the dark
    4. 4. Inoculate 5mL of overnight culture from step 3 in 50mL of same medium
    5. 5. Under constant agitation at 200 rpm at 27°C, culture until OD600 = 0.8–1.2 in the dark
    6. 6. Centrifuge to harvest bacterial culture
    7. 7. Wash with induction medium (BG11 + 100 μM acetosyringone, pH 5.6) and dilute to OD600 = 0.5
    8. 8. Pre-culture total of 5 × 106 Chlorella cells from a log-phase culture (OD600 = 0.5–1.0) on BG11 solidified with 1.5% (w/v) bacto-agar at 25°C for 5 days
    9. 9. Harvest bacterial culture with induction medium
    10. 10. Mix algal pellet with 200 μL bacterial suspension
    11. 11. Plate on induction medium solidified with 1.5% (w/v) bacto-agar
    12. 12. Co-cultivate algae with bacteria (3 days, in dark, 25°C)
    13. 13. Harvest cells with 7mL of BG11 supplemented with 500 mg/L cefotaxime and 50 mg/L kanamycin to eliminate Agrobacterium (2 days, in dark, 25°C)
    14. 14. Measure eGFP expression
    15. 15. Plate the remaining cells on selective media with 50 mg/L kanamycin and 500 mg/L cefotaxime
    16. 16. Incubate transformed cells in dark before exposure to light (2 days, 25°C)
    17. 17. Grow cells on LB agar plates to detect any Agrobacterium (7 days in dark, 25°C)


    Fluorescence microplate reader assay (Molino et al., 2018)

    1. 1. Inoculate transformed colony in 1mL BG11 selective media and incubate at 25°C under constant illumination (50 μmol photons/m2/s) and constant agitation at 100–150 rpm on a rotary shaker, culture for 7 days
    2. 2. Transfer 100 μL cells to wells of a black, clear bottom 96-well plate
    3. 3. Set up microplate reader (ThermoFisher Scientific, USA) as table 1
    4. 4. Measure fluorescence using BG11 medium as blank and wild type cells as negative control
    5. 5. Repeat steps 5-7 with supernatant in the Deep-well plate obtained by centrifugation at 3000 ×g for 10 min
    6. 6. The fluorescent signal is normalized by OD600.

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    Fluorescence microscopic observation of EGFP expression (Yang et al., 2015)
    1. The mediums and supplements for microalgae transformation are obtained from Kisan Bio, South Korea.
    1. - eGFP fluorescence was visualized by using a narrow-band filter (Olympus U-FBNA, excitation filter 470–495 nm, barrier filter 510–550 nm).
    2. - Chlorophyll autofluorescence was observed using a wide-band filter (Olympus U-FBW, excitation filter 460–495 nm, barrier filter 510 nm)




    References


    Cha, T. S., Yee, W., & Aziz, A. (2011, December 29). Assessment of factors affecting Agrobacterium-mediated genetic transformation of the unicellular green alga, Chlorella vulgaris. World Journal of Microbiology and Biotechnology, 28(4), 1771–1779. https://doi.org/10.1007/s11274-011-0991-0

    Kim, M., Kim, J., Kim, S., & Jin, E. (2020). Heterologous Gene Expression System Using the Cold-Inducible CnAFP Promoter in Chlamydomonas reinhardtii. Journal of Microbiology and Biotechnology, 30(11), 1777–1784. https://doi.org/10.4014/jmb.2007.07024

    Kropat, J., von Gromoff, E. D., Müller, F. W., & Beck, C. F. (1995). Heat shock and light activation of Achlamydomonas HSP70 gene are mediated by independent regulatory pathways. Molecular and General Genetics MGG, 248(6), 727–734. https://doi.org/10.1007/bf02191713

    Molino, J. V., de Carvalho, J. C., & Mayfield, S. (2018). Evaluation of secretion reporters to microalgae biotechnology: Blue to Red Fluorescent Proteins. Algal Research, 31, 252–261. https://doi.org/10.1016/j.algal.2018.02.018

    Reyes, A., Farías, M. A., Corrales, N., Tognarelli, E., & González, P. A. (2022). Herpes simplex viruses type 1 and type 2. Encyclopedia of Infection and Immunity, 12–36. https://doi.org/10.1016/b978-0-12-818731-9.00062-8

    Sauer, B., & Henderson, N. (1988). Site-specific DNA recombination in mammalian cells by the cre recombinase of bacteriophage P1. Proceedings of the National Academy of Sciences, 85(14), 5166–5170. https://doi.org/10.1073/pnas.85.14.5166

    Thomson, J. G., Chan, R., Thilmony, R., Yau, Y.-Y., & Ow, D. W. (2010). PHIC31 recombination system demonstrates heritable germinal transmission of site-specific excision from the Arabidopsis genome. BMC Biotechnology, 10(1), 17. https://doi.org/10.1186/1472-6750-10-17

    Yang, B., Liu, J., Liu, B., Sun, P., Ma, X., Jiang, Y., Wei, D., & Chen, F. (2015). Development of a stable genetic system for chlorella vulgaris—a promising green alga for CO2 biomitigation. Algal Research, 12, 134–141. https://doi.org/10.1016/j.algal.2015.08.012

    You, Y. S., Marella, H., Zentella, R., Zhou, Y., Ulmasov, T., Ho, T. H. D., & Quatrano, R. S. (2006). Use of Bacterial Quorum-Sensing Components to Regulate Gene Expression in Plants. Plant Physiology, 140(4), 1205–1212. https://doi.org/10.1104/pp.105.074666