Team:Toulouse INSA-UPS/Methods

Medium


LB∕LBA


Materials
  • 10 g/L tryptone

  • 5 g/L yeast extract

  • 5 g/L NaCl

  • (15 g/L agar bacteriological agar type E)

Dissolve in demineralized water, stir and autoclave.


YPD/YPDA


Materials
  • 10 g/L yeast extract

  • 20 g/L bacto-peptone

  • 20 g/L glucose or galactose

  • (20 g/L bacteriological agar type E)

Dissolve in demineralized water, stir and autoclave.


BGM (from the Marburg 2019 team)


Materials
  • Stock 1 (100X): (autoclave)

  • Material

    Concentration

    Na2Mg EDTA

    4.84 g/L

    Ferric ammonium citrate

    6.29 g/L

    CaCl2 x 2 H2O

    17.94 g/L

    Citric acid x 1 H2O

    3.00 g/L


  • Stock 2 (100X): (autoclave)

  • Material

    Concentration

    MgSO4 x 7 H2O  

      37.46 g/L


  • Stock 3 (100X): (autoclave)

  • Material

    Concentration

    K2HPO4

    10.45 g/L

    KH2PO4

    8.17 g/L


  • (Stock 4 (500X): (autoclave)

  • Material

    Concentration

    H3BO3

    7.14 g/L

    MnCl2 x 4 H2O

    4.52 g/L

    ZnSO4 x 7 H2O

    311 mg/L

    CuSO4 x 5 H2O

    126 mg/L

    NaMoO4

    122 mg/L

    CoCl2x 6 H2O
    solve first in 30 mL water and add to stock 4

    975 mg/L


Combine stock solutions and add 1 M HEPES/NaOH buffer (pH 8.0) stock solution to a final concentration of 20 mM. Add 8.16 g of NaNO3 per liter of medium.
For solid media add 1.4 % Agar.
Autoclave. Add filter sterilized Na2S2O3 to a final concentration of 1 mM to 5X BGM-Agar.

Co-culture medium


Our co-culture medium was made with BGM 1X medium to which we added:

Material

Concentration

Yeast extract w/o amino acids

1.2 g/L

NaCl

100 nM


Tips

We could have filtered the solutions


BG−11


In order to realize our BG11 we ordered the medium in powder form from PhytoTech Lab.
The medium was then prepared by mixing 1.67 g of powder in 1L of H2O milliQ The solution was then autoclaved before use.


Electrophoresis gel (0.8%):


Dissolve 8 g/L agarose D-5 in TAE 1X

Molecular biology


GeneJET Plasmid Miniprep Kit (ThermoFischer)


Materials
  • 1.5 mL Eppendorf tubes

  • Table-top Centrifuge

  • Kit Resuspension Solution

  • Kit Lysis Solution

  • Kit Neutralization Solution

  • Kit Wash Solution

  • Kit Elution Buffer


Protocol
  1. Resuspend cells, lyse and neutralize:
    Add to the pelleted cells:
    250 μL of Resuspension Solution and vortex
    250 μL of Lysis Solution and invert the tube 4-6 times
    350 μL of Neutralization Solution and invert the tube 4-6 times
    Centrifuge 5 minutes at 12,000 g

  2. Bind DNA:
    Transfer the supernatant to the Thermo Scientific GeneJET Spin Column.
    Centrifuge 1 minute at 12,000 g

  3. Wash the column:
    Add 500 μL of Wash Solution and centrifuge for 30-60 s at 12,000 g
    Discard the flow-through
    Repeat twice
    Centrifuge empty column for 1 minute at 12,000 g to get rid of Wash buffer

  4. Elute purified DNA:
    Transfer the column into a new tube
    Add 50 μL of Elution Buffer to the column and incubate 2 minutes
    Centrifuge 2 minutes at 12,000 g
    Collect the flow-through

  5. Tips

    Wait ~10 min with the tube open to remove all the remaining ethanol


  6. Quantity of DNA recovered (with a Nanodrop)


PCR


Materials
  • PCR thermocycler

  • 0.2 mL PCR tubes

  • Primers (both forward and feverse)

  • Template DNA

  • DNA polymerase

  • Nuclease-Free Water


Using ™ NebCalculator is highly recommended.


Q5

This polymerase was used to amplify our fragments in order to perform our In Fusion.

Component

25 μL

50 μL

Final concentration

Q5 High-Fidelity 2X Master Mix

12.5 μL

25 μL

1X

10 μM Forward primer

1.25 μL

2.5 μL

0.5 μM

10 μM Reverse primer

1.25 μL

2.5 μL

0.5 μM

Template DNA

variable

variable

0.5 ng genomic 100 pg vector

Nuclease-Free Water

QSP 25 μL

QSP 50 μL



OneTaq

This polymerase was used for screening to verify the sizes of our fragments.

Step

Temperature

Time

Initial denaturation

98°C

30 seconds

25-35 Cycles

98°C

10 seconds

50-72°C

30 seconds

72°C

30 seconds/kb

Final extension

72°C

2 minutes

Hold

4-10°C



CloneAmp

This polymerase was used for screening to verify the sizes of our fragments.

Component

25 μL

50 μL

Final concentration

One Taq Quick-Load 2X Master Mix

12.5 μL

25 μL

1X

10 μM Forward primer

0.5 μL

1 μL

0.2 μM

10 μM Reverse primer

0.5 μL

1 μL

0.2 μM

Template DNA

variable

variable

<1,000 ng

Nuclease-Free Water

QSP 25 μL

QSP 50 μL


Step

Temperature

Time

Initial denaturation

94°C

30 seconds

25-35 Cycles

94°C

30 seconds

45-68°C

45 seconds

68°C

1 minute/kb

Final extension

68°C

5 minutes

Hold

4-10°C



Bacteria colony PCR

To perform colony PCR, colonies of bacteria were collected, thanks to toothpicks, on boxes after 1-2 days of incubation. The toothpicks were then directly plunged into the PCR tubes with the PCR mix. The tubes were then put in the thermocyclers to perform the PCR.


Gel verification and EtBr staining procedure


Agarose gel migration at 100V during 25 min using Gel Loading Dye, Purple (6X) by NEB, and 1kb plus ladder as molecular weight marker by NEB.
After migration of PCR products on 0.8% agarose gels, the gels were treated in BET baths for 10 minutes to stain the DNA and to reveal them under UV light.


NucleoSpin-Gel-and-PCR-Clean-up kit by NucleoSpin


Materials
  • Kit buffers NT1 and NT3

  • H2O milliQ

  • 1.5 mL Eppendorf tubes

  • Table-top centrifuge


Protocol
  1. Excise DNA fragment and solubilize gel slice in twice the weighted volume with NT1

  2. Incubate 10 min at 50°C

  3. Centrifuge 30 s at 11,000 g

  4. Add 700 μL of NT3, and centrifuge 30 s at 11,000 g

  5. Repeat step 4

  6. Centrifuge 1 min at 11,000 g

  7. Add 20 μL of milliQ water, wait for 2 min at room temperature

  8. Place the column into a new 1.5 mL eppendorf and centrifuge 1 min at 11,000 g


In Fusion HD Cloning Kit (Takara)


Materials
  • Stellar competent cells

  • Falcon tube

  • 42°C water bath

  • Kit SOC medium

  • 37°C incubator with and without agitation

  • Thermcycler

  • Kit control insert

  • Kit control vector

  • 5X In-Fusion HD Enzyme Premix


Protocol
  1. Purify fragment (insert or linearized vector) by gel extraction followed by spin-column purification using a silica-based purification system, such as the NucleoSpin Gel and PCR Clean-Up kit

  2. Plan the In-Fusion cloning reaction. Good cloning efficiency is achieved when using 50–200 ng of vector and inserts, respectively. More is not better. Use the table below for reaction recommendations

    Component

    Cloning

    Negative Control

    Positive Control

    Purified PCR fragment

    10-200 ng

    2 μL of 2 kb control insert

    Linearized vector

    50-500 ng

    1 μL

    1 μL of pUC19 control vector

    5X In-Fusion HD Enzyme Premix

    2 μL

    2 μL

    2 μL

    Deionized Water

    QSP 10 μL

    QSP 10 μL

    QSP 10 μL

  3. Set up the In-Fusion cloning reaction:
    2 μL 5X In-Fusion HD Enzyme Premix
    x μL* Linearized vector
    x μL* Purified PCR insert
    x μL* Purified PCR insert
    x μL dH2O (as needed)
    10 μL Total volume
    * For reactions with larger combined volumes of vector and PCR insert (>7 μL of vector + insert), double the amount of enzyme premix, and add deionized water H2O to a total volume of 20 μL

  4. Incubate the reaction for 15 min at 50°C, then place on ice

    Tips

    This time can be increased to 30 minutes


  5. Thaw Stellar Competent Cells in an ice bath just before use

  6. After thawing, mix gently to ensure even distribution, and then transfer 50 μL of competent cells into a 14-mL round-bottom tube (falcon tube). Do not vortex

  7. Add no more than 5 ng of DNA for transformation.

  8. Place the column into a new 1.5 mL eppendorf and centrifuge 1 min at 11,000 g

  9. Place tubes on ice for 30 min

  10. Heat shock the cells for exactly 45 s at 42°C and then on ice for 1-2 min

  11. Add SOC medium to bring the final volume to 500 μL. SOC medium should be warmed to 37°C before using

  12. Incubate by shaking (160–225 rpm) for 1 hr at 37°C

  13. Plate an appropriate amount of culture on a selective medium
    NOTE: For a plate with a diameter of 9 cm, plate 100 μL. Plating is accomplished by spreading cells on selective medium [e.g., LB agar + Ampicillin (50–100 μg/mL)]. The medium should also contain X-Gal (40 μg/mL) for plasmids that permit blue/white screening of transformants

  14. Incubate overnight at 37°C


Enzymatic digestion


Materials
  • NEB restriction enzymes

  • Template DNA

  • NEB Cutsmart Buffer 10X

  • 37°C incubator


Protocol
  1. Cutsmart Buffer 10X 2 μL

  2. DNA around 100 ng

  3. Enzyme 1 μL

  4. H2O milliQ qsp 20 μL

  5. 2h incubation at 37°C


Mix2Seq Kit NightXpress (eurofins Genomics)


Materials
  • Eurofins barcoded tubes

  • Primer

  • Template DNA

  • H2O milliQ


Protocol
  1. In the barcoded tube, add 15 μL of purified DNA (the quantity of DNA should not exceed 100 ng, we recommend 75 ng).

  2. Add 2 μL of primer (one tube for one primer) at a concentration of 10 ng/μL. The total volume should be 17 μL.

  3. Once the results are received, align with the “Template alignment” on benchling in order to compare with reference sequence

Yeast protocol



Yeast integration protocol provided by the LRSV


Materials
  • 100°C dry or water bath

  • Filter-sterile plate buffer (40% PEG4000, 100 mM LiAc, 10 mM Tris-HCl, 1 mM EDTA)

  • Filter-sterile 1 M DTT

  • YPD broth and YPD agar (with and without the selection parameter)

  • Denatured single stranded DNA (salmon sperm DNA) b(y heating 5 minutes at 100°C, then keep on ice before use)


Protocol
  1. Grow a 5 mL overnight recipient yeast culture in a shaking heat chamber at 30°C (with or without antibiotic, depending on the yeast strain)

  2. With the overnight culture (at OD=0.15), inoculate 100 mL of prewarmed YPD broth. Grow to reach OD 0,6-1

  3. Split the culture according to the number of constructs to be co-transformed in 50 mL falcon tube (one falcon = one transformation). Centrifuge 6 min at 6000 rpm

  4. Remove the supernatant and add to the cells:
    10 μL of SSDNA at a concentration of 10 mg/mL
    1 μg to 2 μg DNA (optimum is 1 μg)
    500 μL plate buffer

  5. Transfer the mix in a 1.5 mL eppendorf and vortex vigorously

  6. Add 20 μL of sterile DTT 1 M and vorte

  7. Incubate at 21°C, 400 rpm overnight, as long as possible (15-20 hours)

  8. Centrifuge 30 s at 5000 rpm

  9. Remove the supernatant and gently resuspend the cells in 200-500 μL YPD

  10. Spread on selective medium and incubate at 30°C for 2 to 5 days


Yeast Integration Takara Protocol


Materials
  • Yeast cells

  • YPD medium

  • Flask 1 L

  • 30°C incubator with agitation

  • Table-top Centrifuge

  • 1X TE/1X LiAc solution

  • Template DNA

  • Vortex

  • PEG/LiAc solution

  • DMSO

  • 1X PEG solution

  • 42°C water bath

  • Selective YPD agar plate


Protocol
  1. Inoculate 1 mL of YPD with several 2–3 mm diameter colonies

  2. Vortex vigorously for 5 min to disperse clumps

  3. Transfer into a flask containing 50 mL of YPD or the appropriate SD medium

  4. Incubate at 30°C for 16–18 hr with shaking at 250 rpm to reach stationary phase (OD600>1.5)

  5. Transfer 30 mL of overnight culture to a flask containing 300 mL of YPD. Check the OD600 of the diluted culture and, if necessary, add more of the overnight culture to bring the OD600 up to 0.2–0.3

  6. Incubate at 30°C for 3 hr with shaking (230 rpm). At this point, the OD600 should be 0.4–0.6

  7. Place cells in 50-mL tubes and centrifuge at 1,000 g for 5 min at room temperature (20–21°C)

  8. Discard the supernatant and thoroughly resuspend the cell pellets in sterile TE or distilled H2O. Pool the cells into one tube (final volume 25–50 mL)

  9. Centrifuge at 1,000 g for 5 min at room temperature.

  10. Decant the supernatant.

  11. Resuspend the cell pellet in 1.5 mL of freshly prepared, sterile 1X TE/1X LiAc

  12. Add 0.1 μg of plasmid DNA and 0.1 mg of carrier DNA to a fresh 1.5-mL tube and mix.
    Notes:
    • For simultaneous cotransformation (using two different plasmids),use 0.1 μg of each plasmid (an approximately equal molar ratio),in addition to the 0.1 mg of carrier DNA.
    • For transformations to integrate a reporter vector, use at least 1 μg of linearized plasmid DNA in addition to the carrier DNA.

  13. Mix 0.1 mL of yeast competent cells to each DNA tube and mix well by vortexing

  14. Add 0.6 mL of sterile PEG/LiAc solution to each tube and vortex at high speed for 10 s to mix

  15. Incubate at 30°C for 30 min with shaking at 200 rpm

  16. Add 70 μL of DMSO, mix well by gentle inversion (do not vortex)

  17. Heat shock for 15 min in a 42°C water bath

  18. Chill cells on ice for 1–2 min

  19. Centrifuge cells for 5 s at 14,000 rpm at room temperature. Remove the supernatant

  20. Resuspend cells in 0.5 mL of sterile 1X TE buffer

  21. Plate 100 μL on each YPD agar plate that will select for the desired transformants. To ensure that you will obtain a plate with well-separated colonies, also spread 100 μL of a 1:1000, 1:100, and 1:10 dilution on YPD agar plates. These will also serve as controls for cotransformation efficiency. Note: If you are performing a cotransformation, plate controls to check transformation efficiency and markers of each plasmid. On separate 100-mm plates, spread 1 μL (diluted in 100 μL H2O) on medium that will select for a single type of plasmid.

  22. Incubate plates, upside-down, at 30°C until colonies appear (generally, 2–4 days).


Yeast colony PCR


Materials
  • Oese or toothpick

  • NaOH 20 mM

  • Thermocycler

  • Vortex

  • Table-top centrifuge


Protocol
  1. Check the transformation plates after 2-5 days of growth at 30°.

  2. Take a small amount of fresh biomass and resuspend in 15 μL of 20 mM NaOH

  3. Incubate 15 min at 96°C

  4. Vortex briefly and spin down the cells 5 minutes at 6000 g

  5. Mix the following in a PCR tube (for 10 reactions):
    50 μL 2xOneTaq Master Mix (New England Biolabs)
    10 μM primer 1
    10 μM primer 2
    20 μL water

  6. Add 1 μL of the denatured biomass to each tube containing 9 μL of the PCR premix

  7. Run the following PCR program: 94°C for 1 min 35 cycles of [94°C for 20 seconds 50°C for 30 seconds 68°C for 1 min/kb of the PCR product] 68°C for 7 min 10°C hold

  8. Analyze the products on 0.8% agarose gel

Cyanobacteria protocol


Transformation of the Helper Strain


Materials
  • Competent cells

  • 1.5 mL Eppendorf tubes

  • Ice

  • 42°C water bath

  • SOC medium

  • 37°C incubator with and without agitation

  • Selective agar plates


Protocol
  1. Thaw frozen competent cells on ice

  2. Add 1-50 ng of DNA or 10 pg of competents cells control DNA (supplied as 0.1 ng/μL) per 50 μL tube of competent cells, quickly flick the tube several times (use the competent cells control DNA to determine transformation efficiency)

  3. Keep tubes on ice for 30 minutes

  4. Heat-shock the cells for 15-20 seconds in a water bath at exactly 42°C, do not shake

  5. Immediately place the tubes on ice for 2 minutes

  6. Add 450 μL of room temperature SOC medium to each transformation reaction and incubate for 60 minutes at 37°C with shaking.

  7. For each transformation reaction, dilute the cells 1:10 and 1:100 and spread dilutions onto agar plates containing antibiotics. Incubate the plates at 37°C for 12-14 hours or overnight. If using BL21 (DE3) pLysS competent cells, do not dilute; spread 100 μL of these cells directly onto agar plates containing antibiotics.


Triparental conjugation protocol


Materials
  • Strains UTEX 2973, prK2013 and HB101

  • Table-top Centrifuge

  • 37°C Incubator

  • 40°C Incubator with high lighting

  • Sterile filters

  • BG11 agar plate with and without spectinomycin

  • BG11 broth

  • Flask 100 mL

  • Kanamycine

  • Sterile loop


Protocol

1. Growth of the cyanobacterial culture (day 1)

  1. Prepare BG11 medium according to Lea-Smith et al., and agar plates with LB-BG11 and BG11+Kan50.

  2. Set up a fresh culture of Synechocystis PCC 6803 or S. elongatus UTEX 2973 by inoculating a 100 mL conical flask of fresh BG11 medium (50 mL) with cells sourced from an axenic BG11 agar plate. Grow S. elongatus UTEX 2973 at 40°C, 300 μmol photons m-2 s-1 at 100 rpm. Grow cultures until OD750nm = 0.5−1.5 (typically 1−2 days).

NOTE: S. elongatus UTEX 2973 cultures can be grown at 40°C in high light intensities (e.g., 2000 μmol photons m-2 s-1)

2. Growth of helper and cargo E. coli strains (day 2)

  1. Inoculate LB medium containing ampicillin (final concentration 100 μg/mL) and chloramphenicol (final concentration 25 μg/mL) with a MC1061 E. coli strain containing vectors pRK24 and pRL528 (i.e., the helper strain) and grow at 37°C overnight at 225 rpm in a shaking incubator. Grow up a sufficient volume of helper strain culture, assuming 1 mL of culture is required per conjugation.

  2. Inoculate LB medium (5 mL) containing appropriate antibiotics with the E. coli culture carrying the cargo vector (i.e., a Level T vector). Grow the culture at 37°C overnight at 225 rpm in a shaking incubator.

3. Conjugal transfer (triparental mating) (day 3)

  1. Prepare the E. coli helper and cargo strains. Centrifuge the helper and the cargo E. coli overnight cultures at 3,000 g for 10 min at room temperature. Discard the supernatant without disturbing the cell pellet.

  2. Wash the pellet by adding fresh LB medium without antibiotics. Use the same volume as the initial culture. Resuspend the pellet by gently pipetting up and down. Do not vortex the culture. Repeat this step 3x to remove residual antibiotics from the overnight culture.

  3. Centrifuge the resuspended culture (as in step 3.3.1), discard the supernatant and resuspend in half the volume of LB medium of the initial culture volume (e.g., 2.5 mL if the overnight culture was 5 mL). Combine 450 μL of the helper strain with 450 μL of the cargo strain in a 2 mL tube and set aside (leave at RT) until step 3.3.6.

  4. Prepare the cyanobacterial culture. For each conjugation reaction, use 1 mL of cyanobacterial culture (OD750nm = 0.5−1.5).

  5. Centrifuge the required total volume of cyanobacterial culture at 1,500 g for 10 min at RT, then discard the supernatant carefully without disturbing the cell pellet. Wash the pellet by adding fresh BG11 medium of the same initial volume. Resuspend the pellet by gently pipetting up and down, do not vortex the culture. Repeat this step 3x and set the washed culture aside.

  6. Add an aliquot of washed cyanobacterial culture (900 μL) to the combined E. coli strains (helper and cargo) (900 μL) in a 2 mL tube. Mix the cultures by gently pipetting up and down. Do not vortex. Incubate the mixture at RT for 30 min for Synechocystis PCC 6803 or 2 hr for S. elongatus UTEX 2973.

  7. Centrifuge the mixture at 1,500 g for 10 min at RT. Remove 1.6 mL of the supernatant. Resuspend the pellet in the remaining ~200 μL of supernatant. Place one 0.45 μm membrane filter on an LB-BG11 agar plate lacking antibiotics (section 8). Carefully spread 200 μL of the E. coli cyanobacterial culture mix on the membrane with a sterile spreader or a sterile bended tip and seal the plate with paraffin film

  8. Incubate the LB-BG11 plate with the membrane for 24 hr. Maintain membranes with Synechocystis PCC 6803 cultures at 30°C, 100 μmol photons m-2 s-1. Maintain membranes with S. elongatus UTEX 2973 cultures at 40°C in 150 μmol photons m-2 s-1.

2. Growth of helper and cargo E. coli strains (day 2)

  1. Inoculate LB medium containing ampicillin (final concentration 100 μg/mL) and chloramphenicol (final concentration 25 μg/mL) with a MC1061 E. coli strain containing vectors pRK24 and pRL528 (i.e., the helper strain) and grow at 37°C overnight at 225 rpm in a shaking incubator. Grow up a sufficient volume of helper strain culture, assuming 1 mL of culture is required per conjugation.

  2. Inoculate LB medium (5 mL) containing appropriate antibiotics with the E. coli culture carrying the cargo vector (i.e., a Level T vector). Grow the culture at 37°C overnight at 225 rpm in a shaking incubator.

4. Membrane transfer

  1. After 24 hr, carefully transfer the membrane using flame-sterilized forceps to a fresh BG11 agar plate containing appropriate antibiotics (section 8) to select for the cargo vector. Seal the plate with paraffin film.

  2. Incubate the BG11 agar plate under appropriate growth conditions, as described above for Synechocystis PCC 6803 or S. elongatus UTEX 2973, until colonies appear. NOTE: Colonies typically appear after 7−14 days for Synechocystis PCC 6803 and 3−7 days for S. elongatus UTEX 2973.

5. Selection of conjugants

NOTE: Only cyanobacteria colonies carrying the cargo vector will be able to grow on the membrane.

  1. Using a heat sterile loop, select at least two individual colonies from the membrane and streak onto a new BG11 agar plate containing appropriate antibiotics (Figure 5C). NOTE: Freshly streaked colonies may still be contaminated with E. coli carried over from conjugation (i.e., if small white colonies are evident on the plate), so two or three additional rounds of re-streaking onto fresh BG11 agar plates typically are needed to obtain an axenic cyanobacterial culture.

  2. Confirm absence of E. coli contamination by inoculating a streak of cyanobacterial culture into a 15 mL centrifuge tube containing 5 mL of LB medium and incubating at 37°C overnight at 225 rpm in a shaking incubator. Following a sufficient growth period (~7 days), pick individual axenic colonies to set up liquid cultures for long-term cryostorage or subsequent experimentation.


Cyanobacteria colony PCR


Method 1


Materials
  • Cyanobacteria cells

  • DMSO

  • Thermocycler


Protocol
  1. Resuspend a single colony in 10 μL DMSO.

  2. Incubate 5 min at 95°C.

  3. Use 1-1.5 μL of this mix as a template for PCR

Method 2


Materials
  • Cyanobacteria cells

  • Sterile water

  • -80°C freezer

  • 60°C water bath

  • Thermoccycler


Protocol
  1. Resuspend one colony in 10 μL sterile water.

  2. Do 3 cycles of freeze (-80°C) and thaw (60°C) (5 min each).

  3. Use 1 μL of this suspension as PCR template [For control reactions with plasmid templates, use 0.5 μL]


Monitoring growth culture


Materials
  • 38°C incubator with shaking

  • LED panel for lighting

  • Flask 100 mL

  • BG11

  • Spectrophotometer


Protocol

All cultures were separated in 2 flasks: one in which all the samples were taken, and the other one only used to inoculate the following cultures. This allowed us to always have a non-contaminated culture because we did not work with it. OD monitoring was performed at 750 nm over several days, with regular sampling. The light intensity of the cultures was measured with a LI-COR lightmeter. The device was placed in the incubator to measure the illumination of the cultures.

Bioreactor


Protocol

Total volume of culture: 1.5 L

  1. 20 mL of culture flasks were inoculated with single colonies. These exponentially growing cultures were used to inoculate 200 mL of culture in 1 L baffled erlens. These erlen cultures were finally used to inoculate the reactors.

  2. Samples were taken three times a day, the OD750 was measured and HPLC vials were prepared (centrifugation 10 min at maximum speed and filtration of the supernatant with 0.45 micron filters). The HPLC analysis was Aminex HPX-87K Column. This potassium-form, 300 x 7.8 mm column and H2O milliQ as mobile phase. to check the sucrose secretion.

For strain cscB:

  • BG11 media supplemented with 150 mM of NaCl

  • pH 7.5 (regulated with HCl and NaOH respectively)

  • Temperature 41°C

  • 5 % CO2

  • Light: Warm white light (LED) between 1500 μE (front of the reactor) and 200 μE (back of the reactor)

  • IPTG 1 mM (added in the reactors)

  • Kanamycin (10 μg/μL)

For strain cscB sps spp:

  • BG11 media

  • pH 7.5 (regulated with HCl and NaOH respectively)

  • Temperature 41°C

  • 5 % CO2

  • Light: Warm white light (LED) between 1500 μE (front of the reactor) and 200 μE (back of the reactor)

Sampling

The samples were collected with a syringe.
Sampling tube connects the bioreactor to the sampling chamber. Output tube connect the sampling chamber to the outlet, where the sample can be collected in a container. Aspiration tube connects the sampling chamber to the syringe.

To take a sample:

  1. Unclamp the sampling and clamp the outlet tube.

  2. Aspirate air with the syringe, this will fill the sampling chamber.

  3. Clamp the sample tube and unclamp the output tube.

  4. Evacuate the air from the syringe, causing the sample to flow out of the chamber through the output tube. The sample can be recovered at the outlet of the tube.

To collect samples:

  1. Pinch the output tube and suck in air with the syringe.

  2. Pinch the sampling tube, place a recipient tuve under the output tube to collect the sample and empty the air from the syringe.

Detection


HPLC


Sucrose

To analyze sucrose secretion, 1 mL of culture was collected and centrifuged at maximum speed for 5 minutes. The supernatant was collected and then filtered through a 0.2 μm filter. The sucrose secretion was quantified by HPLC with an Aminex HPX-87K Column This potassium-form, 300 x 7.8 mm column and mQ water as mobile phase. Column was kept at 70°C, flow rate 0.6 mL/min and analysis time 20 minutes.


Carotene

To quantify carotènes in our culture, 1 mL of culture was centrifuged and the supernatant eliminated. The pellet was resuspended in 1 mL acetone and the cells were broken with 500 μL of glass beads in a FastPrep-24™ Classic. The mechanical lysis conditions were: one cycle of 40 s of shaking at 6m/s. After centrifugation, the supernatants were analyzed on a C18 RP HPLC column,Thermo Scientifc™ Hypersil C18 GOLD™, 3 μm, and 2.1×100 mm column, with a mixture of acetonitrile:methanol:isopropyl (85:10:5 v/v) as eluant. Column was kept at 20°C, flow rate 0.5 mL/min and analysis time 15 minutes.



GC-MS


The analyses were performed on a GC-MS Trace 1310-ISQ (Thermofisher) equipped with a single quadrupole mass spectrometer with Helium as carrier gas. The column used was a ZB-1701 (Phenomenex - 7HG-G006-05-C) with the following dimensions: Length: 30 m, Internal diameter: 0.25 mm, Film thickness: 0.15 mm).

The analysis conditions are listed in the followed table:

Parameters

Unity

Values

Injector temperature

[°C]

250

Mobile phase flow

Mobile phase flow [mL.min-1]

0.9

Oven temperature gradient

[°C.min-1]

7, 4, 25

Transfer tube temperature

[°C]

250

Source temperature

[°C]

300

m/z range followed

[/]

35 to 700

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