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PCR targeting system in__ Streptomyces

PCR targeting system in Streptomyces coelicolor A3(2)

Bertolt Gust, Tobias Kieser and Keith Chater, John Innes Centre, Norwich Research Park, Colney, Norwich NR47UH, UK, Tel: +44 (0)1603 452751 Fax: +44 (0)1603 456844

Introduction

Many bacteria are not readily transformable with linear DNA because of the presence

of the intracellular recBCD exonuclease that degrades linear DNA. However, the λ RED (gam, bet, exo) functions promote a greatly enhanced rate of recombination when using linear DNA. By exploiting this, Datsenko and Wanner (2000) made 40 different disruptions on the E. coli chromosome by replacing the wild-type sequences with a selectable marker generated by PCR using primers with 36 nt homology extensions.

The strategy for PCR-targeting for mutagenesis of Streptomyces coelicolor is to replace a chromosomal sequence within a S. coelicolor cosmid (Redenbach et al., 1996) by a selectable marker that has been generated by PCR using primers with 39 nt homology extensions. The inclusion of oriT (RK2) in the disruption cassette allows conjugation to be used to introduce the PCR targeted cosmid DNA into S. coelicolor. Conjugation is much more efficient than transformation of protoplasts and it is readily applicable to many actinomycetes (Matsushima et al., 1994). The potent methyl-specific restriction system of S. coelicolor is circumvented by passaging DNA through a methylation-deficient E. coli host such as ET12567 (MacNeil et al., 1992). Vectors containing oriT (RK2; Pansegrau et al., 1994) are mobilisable in trans in E. coli by the self-transmissible pUB307 (Bennett et al., 1977, Flett et al., 1997) or the non-transmissible pUZ8002, which lacks a cis-acting function for its own transfer (Kieser et al., 2000).

To adapt the procedure of λ RED mediated recombination for Streptomyces, cassettes

for gene disruptions were constructed that can be selected both in E. coli and in Streptomyces (Table 1). After a single disruption with an oriT-containing cassette, further disruptions can be performed on the same cosmid using oriT-free cassettes containing alternative selective markers. The λ RED recombination plasmid pKD20

(E. coli Genetic Stock Center CGSC Strain # 7637) was modified by replacing the ampicillin resistance gene bla with the chloramphenicol resistance gene cat, generating pIJ790, to permit selection in the presence of Supercos1-derived cosmids (ampicillin and kanamycin resistance).

Name of plasmid Resistance-

marker

Resistance

Concentration

for E. coli oriT Size of template

pIJ773 Fig. 5 aac(3)IV apramycin

50 μg/ml LB + 1382

pIJ778 Fig. 6 aadA

spectinomycin

streptomycin

50 μg/ml LB

50 μg/m LB

+ 1425

pIJ779. aadA spectinomycin-

streptomycin

50 μg/ml LB

- 1057

pIJ780 Fig.7 vph viomycin

30 μg/ml DNA+ 1497

pIJ781 vph viomycin

30 μg/ml DNA- 1622

Table 1: Disruption cassettes containing different resistance markers with and without oriT: All disruption cassettes were cloned into the Eco RV site of pBluescript SK II (+) allowing the isolation of a Eco RI/Hind III fragment for use as template for the PCR reaction. The size of the cassettes includes the 19 bp and 20 bp primer site (see section 2: “primer design”) which are identical in all disruption cassettes. The resistance genes with or without oriT are flanked by FRT sites (FLP recognition targets) which allows FLP-mediated excision of the cassette (see section 7: “FLP-mediated excision of the disruption cassette”).

Fig. 1: Flowchart of gene disruption by PCR-targeting

Protocol (see Flowchart Fig. 1)

Purification of the PCR template (resistance (-oriT) cassette)

Using whole plasmids as templates for the PCR can result in a high proportion of antibiotic-resistant transformants without gene disruption. This is caused by traces of CCC DNA that compete with the linear PCR fragment and result in the occurrence of false positive transformants. Using gel-purified disruption cassettes as templates prevents the occurrence of false positives.

1.Digest ~ 10 μg plasmid DNA (see Table 1) with 50 U Eco RI (Roche) and

50 U Hin dIII (Roche) in 1 X buffer B (Roche) in a 100 μl reaction.

? A 2938 bp vector fragment and a fragment 14 bp larger than the size of the cassette given in Table 1 should be generated.

2.Run the digest on a 20 x 20 x 0.25 cm (100 ml) 1% TAE (1x) agarose gel at

5V/cm for 2 - 3 h in 1x TAE buffer.

?Longer runs exhaust the buffer capacity and destroy the gel unless the buffer is recycled.

3.Cut out the cassette band from the gel and purify using the Qiagen gel

extraction kit. The purified fragment is stored in 10 mM Tris.HCl (pH 8) at a

concentration of 100 ng / μl at –20°C.

4.Absence of plasmid DNA is tested by using 1μl (100 ng) of purified cassette

DNA to transform highly competent E. coli DH5α cells (108/μg). Plate on LB

agar containing 100 μg/ml carbenicillin. If any transformants appear, repeat

steps 2-4.

Design of long PCR primers

For each gene disruption, two long PCR primers (58 nt and 59 nt) are required. Each has at the 5′end 39 nt matching the S. coelicolor sequence adjacent to the gene to be inactivated, and a 3′sequence (19 nt or 20 nt) matching the right or left end of the disruption cassette (all cassettes have the same “right” and “left” ends). The precise positioning of the 39 nt sequence as indicated in Fig. 2 is important for creating in-frame deletions by FLP recombinase-induced excision of the resistance marker (see section 7).

?The 5′- 39 nt sequence of the forward primer (upstream primer; Fig. 2) must be from the coding strand of the gene of interest and its 3’ end must be in the correct reading frame with respect to the replaced gene. The 5′- 39 nt sequence of the reverse primer (downstream primer; Fig. 2) must be from the complementary strand.

?To prevent unwanted recombination, a BlastN search is performed comparing each

39 nt sequence with the “real cosmid” (sequences at the Sanger Centre Homepage in the

folder https://www.wendangku.net/doc/1b11967477.html,/pub/S_coelicolor/cosmid_inserts and on the CD in the folder /S_coelicolor/cosmid inserts). The perfect match should be found but no other matches >30 bp. If necessary, the 39 nt sequence is shifted in 3 nt steps until the above criteria are met.

Fig.2: Designing PCR primers for making an 6

(20bp + 19bp priming sequence + 42bp FLP core recombination site (see Fig.3); no in frame STOP)

in-frame deletion

(the example illustrates a complete deletion)

39 nt from sense strand ending in ATG or GTG start codon

39 nt from anti-sense strand ending in Stop codon

58 nt downstream primer

FLP recombinase (BT340)

PCR amplification of the extended resistance cassette

All PCR amplifications are performed using the Expand high fidelity PCR system according to the manufacturer’s instructions (Roche). Reaction conditions:

?Primers (100 pmoles/μl) 0.5 μl each 50 pmoles each

?Template DNA (100 ng/μl) 0.5 μl 50 ng ≈ 0.06 pmoles

μl

?Buffer

(10x)

?dNTPs (10 mM) 1 μl each 50 μM each

?DMSO (100 %) 2.5 μl 5%

?DNA polymerase (2.5 U/μl) 1 μl 2.5 Units

?Water 36 μl

μl

volume

?Total

Cycle conditions:

1. Denaturation: 94°C, 2 min

2. Denaturation: 94°C, 45 sec

3. Primer annealing: 50°C, 45 sec 10 cycles

4. Extension: 72°C, 90 sec

5. Denaturation: 94°C, 45 sec

6. Primer annealing: 55°C, 45 sec 15 cycles

7. Extension: 72°C, 90 sec

8. Final extension: 72°C, 5 min

5 μl of the PCR product is used for analysis by gel electrophoresis. The expected sizes are 78 bp larger than the sizes of the disruption cassettes listed in Table 1 (because of the 2 x 39 bp 5′-primer extensions). The remaining 45 μl of the PCR product is purified using the Qiagen PCR purification kit according to the manufacturer’s instructions. The PCR product is finally eluted from the columns with 12 μl of water (~200 ng/μl).

Introduction of S. coelicolor cosmid clone into E. coli BW25113/pIJ790 (λ RED recombination plasmid) by electroporation

pIJ790 contains the resistance marker cat (chloramphenicol resistance) and a temperature sensitive origin of replication (requires 30°C for replication).

1.Grow E. coli BW25113/pIJ790 overnight at 30°C in 10 ml LB (Luria-Bertani

medium; Sambrook et al., 1998) containing chloramphenicol (25 μg/ml).

2.Inoculate 100 μl E. coli BW25113/pIJ790 from overnight culture in 10 ml

SOB (Hanahan, 1983) containing 20 mM MgSO4 (add 200 μl of 1M stock to

10 ml SOB) and chloramphenicol (25 μg/ml).

3.Grow for 3-4 h at 30°C shaking at 200 rpm to an OD600 of ~ 0.

4.Recover the cells by centrifugation at 4000 rpm for 5 min at 4°C in a Sorvall

GS3 rotor (or equivalent).

5.Decant medium and resuspend the pellet by gentle mixing in 10 ml ice-cold

10 % glycerol.

6.Centrifuge as above and resuspend pellet in 5 ml ice-cold 10 % glycerol,

centrifuge and decant. Resuspend the cell pellet in the remaining ~ 100 μl

10 % glycerol.

7.Mix 50 μl cell suspension with ~ 100 ng (1-2 μl) of cosmid DNA. Carry out

electroporation in a 0.2 cm ice-cold electroporation cuvette using a BioRad GenePulser II set to: 200 Ω, 25 μF and 2,5 kV. The expected time constant is

4.5 – 4.9 ms.

8.Immediately add 1 ml ice cold LB to shocked cells and incubate shaking for

1h at 30°C.

9.Spread onto LB agar containing carbenicillin (100 μg/ml), kanamycin

(50 μg/ml) and chloramphenicol (25 μg/ml).

10.Incubate overnight at 30°C.

11.Transfer one isolated colony into 5 ml LB containing antibiotics as in (9)

above.

12.Incubate overnight at 30°C. This culture will be used as a pre-culture for

generating competent cells to be transformed with the extended resistance cassette.

PCR targeting of the S. coelicolor cosmid

E. coli BW25113/pIJ790 containing a S. coelicolor cosmid is electro-transformed with the extended resistance cassette. The example described uses the apramycin – oriT disruption cassette from pIJ773. Table 1 lists alternative cassettes and their resistance determinants. 8. Spread onto LB agar containing carbenicillin (100 μg/ml), kanamycin (50 μg/ml) and apramycin (50 μg/ml). If no further gene disruptions will be made on this cosmid, incubate overnight at 37°C to promote the loss of pIJ790. (If further disruptions are planned propagate overnight at 30°C and include chloramphenicol (25 μg/ml) so that pIJ790 is retained).

7. Immediately add 1 ml ice cold LB to shocked cells and incubated shaking 1 h at 37°C (or 30°C if further gene disruptions will be made on the same cosmid; see below).

6. Mix 50 μl cell suspension with ~ 100 ng (1-2 μl) of PCR product. Carry out electroporation in a 0.2 cm ice-cold electroporation cuvette using a BioRad GenePulser II set to: 200 Ω, 25 μF and 2,5 kV. The expected time constant is 4.5 – 4.9 ms.

5. Centrifuge as above and resuspend pellet in 5 ml ice-cold 10 % glycerol,

centrifuge and decant. Resuspend the cell pellet in remaining ~ 100 μl 10 % glycerol.

4. Decant medium and resuspend the pellet by gentle mixing in 10 ml ice-cold 10% glycerol.

3. Recover the cells by centrifugation at 4000 rpm for 5 min at 4°C in a Sorvall GS3 rotor (or equivalent).

2. Grow for 3-4 h at 30°C shaking at 200 rpm to an OD 600 of ~ 0.4.

1. Inoculate a 10 ml SOB (without MgSO 4) culture containing carbenicillin (100

μg/ml), kanamycin (50 μg/ml) and chloramphenicol (25 μg/ml) with 1% of the overnight culture of E. coli BW25113/pIJ790 and the S. coelicolor cosmid. Add 100 μl 1M L-arabinose stock solution (final concentration is 10 mM, induces red genes).

?If no colonies are obtained after 16 h growth at 37°C, repeat the experiment starting with a 50 ml SOB culture instead of 10 ml culture for generating

electrocompetent cells. Try to concentrate the cells as much as possible by

removing all of the remaining 10% glycerol. Resuspend the cell pellet in 50 μl

10% glycerol and use for electroporation.

?After 12 – 16 h growth at 37°C different colony-sizes are observed. Cultivating for longer time results in an increased background of small colonies, which are

false positives. It is important to note that at this stage wild-type and mutant

cosmids exist within one cell. The transformation with a PCR product and its

integration in the cosmid DNA by homologous recombination will not occur in

all copies of the cosmid molecules in one cell. One copy of a cosmid containing

the incoming resistance marker is sufficient for resistance to this antibiotic.

Normally, the larger the size of a colony, the more copies of mutagenised

cosmids are present. Inoculating a large colony in 5 ml LB liquid cultures

containing carbenicillin (100 μg/ml), kanamycin (50 μg/ml) and apramycin

(50 μg/ml) result in a growth at 37°C to a cell density (OD600 ~ 0.1 – 0.3) within

3-4 h (E. coli BW25113 without pIJ790 grows very fast). After 6 h plasmid DNA

can be isolated and tested by restriction analysis and/or PCR using the primers

described below.

?PCR analysis with a primer pair (test primers) priming just ~ 100 bp outside the region affected by homologous recombination will generate the expected

fragment after gene disruption, but will usually also generate the wild-type

fragment, caused by remaining wild-type copies within the same transformant.

These will be lost during the subsequent transformation step into the

methylation-deficient E. coli host ET12567 containing the non-transmissible

plasmid pUZ8002 (this is not a problem anyway because wild-type copies lack

the oriT).

?Notes on viomycin selection: selecting for viomycin R depends critically on the amount of salt in the medium; more viomycin is required at higher salt

concentrations. For a clean selection of E. coli clones, use DNA agar or 2xYT

agar containing 30 μg/ml viomycin (see Kieser et al., 2000).

For multiple gene replacements, choose an oriT-containing disruption cassette for the first knock-out, and a cassette without oriT and different resistance markers for further gene disruptions.

The gene disruption is confirmed by restriction analysis and/or PCR. Cosmid DNA of transformants is isolated from a 6 h, 37°C, 5 ml LB culture containing carbenicillin (100 μg/ml), kanamycin (50 μg/ml) and apramycin (50 μg/ml). Alkaline lysis followed by phenol/chloroform extraction produces cosmid DNA suitable for restriction analysis.

Cosmid CCC DNA isolation

1.Resuspend the cell pellet from 1 ml culture by vortexing in 100 μl solution I

(50 mM Tris/HCl, pH 8; 10 mM EDTA).

2.Immediately add 200 μl solution II (200 mM NaOH; 1% SDS) and mix by

inverting the tubes 10x.

3.Immediately add 150 μl solution III (3 M potassium acetate, pH 5.5) and mix

by inverting the tubes 5x.

4.Spin at full speed in a microcentrifuge for 5 min at room temperature.

5.Immediately extract supernatant with 400 μl phenol/chloroform, vortex 2 min

and spin at full speed in a micro centrifuge for 5 min.

6.Transfer the upper phase and add 600 μl 2-propanol. Leave the tubes on ice

for 10 min.

7.Spin as above and wash the pellet with 200 μl 70% ethanol.

8.Spin as above and leave the tube open for 5 min at room temperature to dry

the pellet. Resuspend the pellet in 50 μl 10mM Tris/HCl (pH 8) and use 10 μl for restriction digest.

?Omitting the phenol/chloroform extraction step results in degradation of the cosmid DNA. Use of miniprep-columns without including a phenol/chloroform

extraction is not recommended.

Verification of positive transformants by PCR requires an additional pair of 18 – 20 nt test primers which anneal 100 – 200 bp upstream and downstream of the 39 bp recombination region. (These primers can also be used later to verify the FLP-mediated excision of the resistance cassette.)

?Primers (100 pmoles/μl) 0.2 μl each 20 pmoles each

?Template DNA (~50 ng/μl) 1 μl 50 ng

μl

?Buffer

(10x)

?dNTPs (10 mM) 1 μl each 50 μM each

?DMSO (100 %) 2.5 μl 5%

?DNA polymerase (2.5 U/μl) 1 μl 2.5 Units

?Water

μl

36.1

μl

volume

?Total

Cycle conditions:

1. Denaturation: 94°C, 2 min

2. Denaturation: 94°C, 45 sec

3. Primer annealing: 55°C, 45 sec 30 cycles

4. Extension: 72°C, 90 sec

5. Final extension: 72°C, 5 min

5 μl of the PCR product is used for gel electrophoresis.

Transfer of the mutant cosmids into Streptomyces

If the target Streptomyces for mutagenesis carries a methyl-sensing restriction system (as is the case for S. coelicolor and S. avermitilis), it is necessary to passage the cosmid containing an apramycin resistance-oriT cassette through a non-methylating E. coli host. To achieve this, it is introduced by transformation into the non-methylating E. coli ET12567 containing the RP4 derivative pUZ8002. The cosmid is then transferred to Streptomyces by intergeneric conjugation (see Table 2 for resistance markers). If the target Streptomyces for mutagenesis does not carry a methyl-sensing restriction system (as is the case for S. lividans), common E. coli strains such as DH5α containing pUZ8002 can be used instead.

Description Name Replication Carb R Cml R Kan R Tet R S. coelicolor

Supercos 1Carb R Kan R

cosmid clones

λ Red plasmid pIJ790 t s Cml R

FLP recombinase

BT340 t s Carb R Cml R

plasmid

OriT- RP4 derivative pUZ8002 Kan R

OriT+ RP4 derivative pUB307 Kan R

Non-methylating E. coli ET12567 Cml R Tet R

Table 2. Resistance markers of vectors, helper plasmids and strains (carbenicillin resistance (Carb R ), chloramphenicol resistance (Cml R), kanamycin resistance (Kan R), tetracycline resistance (Tet R), temperature sensitive replicon (t S)). See Table 1 for replacement cassettes.

1.Prepare competent cells of E. coli ET12567/pUZ8002 grown at 37oC in LB

containing kanamycin (25 μg/ml) and chloramphenicol (25 μg/ml) to maintain selection for pUZ8002 and the dam mutation, respectively. (ET12567 has a doubling time > 30 min.)

?High competence is required when Dam-methylated plasmids are introduced into a dam- strain.

2.Transform competent cells with the oriT-containing cosmid clone, and select

for the incoming plasmid only using apramycin (50 μg/ml) and carbenicillin (100 μg/ml) .

3.Inoculate a colony into 10 ml LB containing apramycin (50 μg/ml),

chloramphenicol (25 μg/ml) and kanamycin (50 μg/ml). Grow overnight at

37oC.

?Chloramphenicol S or Kanamycin S segregants arise frequently among transformants, so set up more than one culture. The kanamycin selection is probably ineffective

because both the cosmid and pUZ8002 confer resistance (Table 2).

4.Inoculate 100 μl overnight culture into 10 ml fresh LB plus antibiotics as

above and grow for ~ 4 h at 37°C to an OD600 of 0.4.

5.Wash the cells twice with 10 ml of LB to remove antibiotics that might inhibit

Streptomyce s, and resuspend in 1 ml of LB.

6.While washing the E. coli cells, for each conjugation add 10 μl (108)

Streptomyces spores to 500 μl 2 × YT broth. Heat shock at 50°C for 10 min,

then allow to cool.

7.Mix 0.5 ml E. coli cell suspension and 0.5 ml heat-shocked spores and spin

briefly. Pour off most of the supernatant, then resuspend the pellet in the

c. 50 μl residual liqui

8.Make a dilution series from 10-1 to 10-4 each step in a total of 100 μl of water.

9.Plate out 100 μl of each dilution on MS agar + 10mM MgCl2 (without

antibiotics) and incubate at 30°C for 16-20 h.

10.Overlay the plate with 1 ml water containing 0.5 mg nalidixic acid (20 μl of

25 mg/ml stock; selectively kills E. coli) and 1.25 mg apramycin (25 μl of

50 mg/ml stock). Use a spreader to lightly distribute the antibiotic solution

evenly. Continue incubation at 30°C.

11.Replica-plate each MS agar plate with single colonies onto DNA plates

containing nalidixic acid (25 μg/ml) and apramycin (50 μg/ml) with and

without kanamycin (50 μg/ml). Double cross-over exconjugants are kanamycin S and apramycin R. (DNA gives fast, non-sporulating growth.)

12.Kanamycin S clones are picked from the DNA plates and streaked for single

colonies on MS agar (promotes sporulation) containing nalidixic acid

(25 μg/ml) and apramycin (50 μg/ml).

13.Confirm kanamycin sensitivity by replica-plating onto DNA plates containing

nalidixic acid (25 μg/ml) with and without kanamycin (50 μg/ml).

14.Purified kanamycin sensitive strains are then verified by PCR and Southern

blot analysis.

? Typically, ~ 10 % of the exconjugants are double cross-over recombinants. The frequency of double cross-overs depends on the length of the flanking regions of homologous DNA on the cosmid. If < 1 kb is left on one side of the disrupted gene, obtaining kanamycin S double cross-over types directly on the conjugation plates may be difficult. It may be necessary to streak out several exconjugants for single colonies on MS agar without antibiotics. After 3-5 days growth replica-plate onto DNA with and without kanamycin.

Concentration in Antibiotic

Stock mg/ml

μl for 1 ml overlay

Final conc. after flooding

μg/ml

MS, DNA μg/ml

R2YE μg/ml

Apramycin 50 25 50 50 50 Kanamycin 50 100 200 50 200 Spectinomycin 200 25 200 400 400 Streptomcyin 10 25 10 10 10 Viomycin 30 25 30 30 NA

Nalidixic acid 25 in

0.3 M NaOH

20 20

Table 3: Antibiotic concentrations for selection on S. coelicolor MS conjugation plates, DNA replica plates or R2YE protoplast regeneration plates (Note some small differences from Kieser et al ., 2000).

FLP-mediated excision of the disruption cassette

The disruption cassettes are flanked by FRT sites (FLP recognition targets). Expression of the FLP-recombinase in E. coli removes the central part of the disruption cassette, leaving behind a 81 bp “scar” sequence which, in the preferred reading frame (bold in Fig. 3), lacks stop codons.

Fig. 3: Sequence of the 81 bp “scar” sequence remaining after FLP-mediated excision of the disruption cassette. The translation of the preferred reading frame is printed bold. The 20 and 19 nt priming sites are underlined and printed in colour. (Fig.

2 explains the determination of the reading frame.)

indicate stop codons,

priming site (20 nt)

priming site (19 nt)

This allows the generation of (hopefully) non-polar, unmarked in-frame deletions and repeated use of the same resistance marker for making multiple knock-outs in the same cosmid or in the same strain. E. coli DH5α cells containing the temperature sensitive FLP recombination plasmid BT340 (Datsenko and Wanner, 2000; can be obtained from the E. coli Genetic Stock Center: CGSC Strain# 7629) are transformed with the mutagenised cosmid DNA (obtained in section 5). BT340 contains ampicillin and chloramphenicol resistance determinants and is temperature sensitive for replication (replicates at 30°C). FLP synthesis and loss of the plasmid are induced at 42°C (Cherepanov and Wackernagel, 1995).

1.Grow E. coli DH5α/BT340 overnight at 30°C in 10 ml LB containing

chloramphenicol (25 μg/ml).

?Transforming E. coli BW25113/cosmid::apramycin (mutagenised cosmid) with the plasmid BT340 is not recommended because the isolates after PCR targeting

may still contain copies of undisrupted cosmid DNA (see page 10, second

paragraph).

2.Inoculate 100 μl E. coli DH5α/BT340 from overnight culture into 10 ml

LB containing chloramphenicol (25 μg/ml).

3.Grow for 3-4 h at 30°C shaking at 200 rpm to an OD600 of ~ 0.

4.Recover the cells by centrifugation at 4000 rpm for 5 min at 4°C in a

Sorvall GS3 rotor (or equivalent).

5.Decant medium and resuspend the pellet by gentle mixing in 10 ml ice-

cold 10 % glycerol.

6.Centrifuge as above and resuspend pellet in 5 ml ice-cold 10 % glycerol,

centrifuge and decant. Resuspend the cell pellet in remaining ~ 100 μl 10% glycerol.

7.Mix 50 μl cell suspension with ~ 100 ng (1-2 μl) of mutagenised cosmid

DNA. Carry out electroporation in a 0.2 cm ice-cold electroporation cuvette using a BioRad GenePulser II set to: 200 Ω, 25 μF and 2,5 kV. The expected time constant is 4.5 – 4.9 ms.

8.Immediately add 1 ml ice cold LB to shocked cells and incubate shaking

for 1 h at 30°C.

9.Spread onto LB agar containing apramycin (50 μg/ml) and

chloramphenicol (25 μg/ml).

10.Incubate for 2 d at 30°C (E. coli DH5α/BT340 grows slowly at 30°C).

11.A single colony is streaked on an LB agar plate without antibiotics for

single colonies and grown overnight at 42°C to induce expression of the FLP recombinase followed by the loss of plasmid BT340.

12.Make two masterplates by streaking 20 – 30 single colonies with a

toothpick first on a LB agar plate containing apramycin (50 μg/ml) and then on a LB agar plate containing kanamycin (50 μg/ml).

13.Grow the masterplates overnight at 37°C. Apramycin S kanamycin R clones

indicate the successful loss of the resistance cassette and are further

verified by restriction and PCR analysis.

?Typically, ~ 10 % of the single colonies after non-selective growth lose the incoming resistance marker and the plasmid BT340 simultaneously.

?Using the same test primers as in section 5 (annealing ~ 100 bp upstream and downstream of the 39 nt primer sequence) should produce a PCR product of

~ 300 bp (200 bp + 81 bp “scar”). PCR fragments can be sequenced using the

amplification primers for verification.

Replacing resistance cassette inserts in S. coelicolor with the unmarked “scar” sequence

The chromosomal apramycin resistance cassette insert in S. coelicolor is replaced by the “scar” sequence. This is achieved by homologous recombination between the chromosome and the corresponding “scar cosmid” prepared in 7. The procedure differs from section 6 because the cosmid lacks oriT, and the desired product is antibiotic sensitive. Therefore, it is necessary to introduce the scar cosmid into Streptomyces by protoplast transformation, and then select for kanamycin resistant Streptomyces containing the entire scar cosmid integrated by a single crossover. Restreaking to kanamycin-free medium, followed by screening for concomitant loss of kanamycin resistance and apramycin resistance, then identifies the desired Streptomyces clones.

Preparation of Streptomyces coelicolor protoplasts

1.Add 25 ml YEME medium to a baffled flask. Add ~ 0.1 ml spore suspension

and required growth factors. Incubate 36-40 h at 30°C in an orbital incubator shaker.

?Cultures of S. lividans and S. coelicolor are ready for harvesting when they start to produce red pigment

2.Pour culture broth into a 20 ml screw cap bottle and spin in the bench

centrifuge (~ 1000 x g, 10 min).

?Before centrifugation, examine the culture for contamination by unicellular bacteria, usually indicated by turbidity: the Streptomyces mycelium sediments

quickly while unicellular contaminants remain suspended. In case of doubt, use the microscope.

3.Discard the supernatant carefully; the pellet is easily disturbed.

?If the mycelium does not pellet add 5 ml sterile water to reduce the density of the medium and centrifuge again.

4.Resuspend pellet in 15 ml 10.3% sucrose and spin in bench centrifuge as

above. Discard supernatant.

5.Repeat step 4.

?The mycelial pellet, without added liquid, can be stored frozen at –20°C

6.Resuspend mycelium in 4 ml lysozyme solution (1 mg/ml P buffer, filter

sterilised); incubate at 30°C, 15-60 min.

7.Draw in and out of a 5 ml pipette three times and incubate for a further 15

min.

?This helps to free protoplasts from the mycelium so that they will pass through the cotton wool filter used in step9. At least with S. lividans, it is possible to obtain transformants with unfiltered material, but the washing (steps 9-10) is still needed to remove lysozyme.

8.Add 5 m1 P buffer. Repeat step 7.

9.Filter protoplasts through cotton wool (using a filter tube) and transfer to a

plastic tube.

10.Sediment protoplasts gently by spinning in a bench centrifuge (~ 1000 x g, 7

min).

11.Discard supernatant and suspend protoplasts in 1 ml P buffer.

?At this and any other steps when pelleted protoplasts are to be resuspended, resuspend in the remaining drop of liquid by tapping the side of the tube repeatedly with a finger until the protoplasts are dispersed to form a creamy suspension, then add the suspending P buffer (otherwise the protoplast pellet is difficult to disperse).

Avoid vortexing, which induces foaming and consequent lysis. To freeze the protoplasts for storage, place samples of the protoplast suspension in small plastic tubes, close them and place them in ice in a plastic beaker. Place the beaker at –70°C overnight. Free the frozen protoplasts in their tubes from the ice and store at –70°C.

To thaw, shake the frozen tube under running warm water (i.e. freeze slowly, thaw quickly). To assess the proportion of non-protoplasted units in the suspension, samples can be diluted in parallel in P buffer and in dilute detergent (~ 0.01% SDS) and plated on regeneration plates. Any colonies arising after dilution in detergent are likely to have arisen from non-protoplasted units.

Rapid small-scale transformation of Streptomyces coelicolor

1.Dispense 50 μl samples of protoplasts (~ 1010/ml) into as many tubes as there

are transformations.

?We usually spin the protoplasts down immediately before the transformation experiment. This eliminates substances that may have leaked out of the protoplasts

during storage and the contents of protoplasts which have lysed spontaneously

(which may include nucleases).

https://www.wendangku.net/doc/1b11967477.html,plete steps 2a-c for each transformation individually.

a.Add up to 5 μl DNA solution to protoplasts and mix immediately by

tapping tube.

b.Add 200 μl 25% PEG 1000 in P buffer and mix by pipetting up and

down four times (be careful not to contaminate the barrel of the

pipette).

c.Spread protoplast suspension (100-200 μl) on two dried R2YE plates.

Use P buffer to make dilutions if required.

?l ml glass pipettes can be used instead of spreaders. The solution will spread to some extent by itself if the plates are left on a horizontal surface.

3.Incubate plates at 30°C. After 14-20 h, flood for kanamycin selection. Score

for resistant colonies after 3 d.

4.Select single colony and streak non-selectively for single colonies on MS agar

plates and grow 3-4 d at 30°C.

5.Replica-plate to DNA agar plates with apramycin (50 μg/ml) or kanamycin

(50 μg/ml) to screen for apramycin S and kanamycin S transformants.