Lambda-red mediated recombination using ssDNA

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Lambda-red mediated recombination using ssDNA

Lambda-red mediated recombination using ssDNA can be used to introduce precise mutations into the genome of Streptomyces strains. These mutations are usually to introduce single nucleotide changes (e.g. to introduce codon changes to alter amino acids or introduce premature stop codons), or small insertions or deletions. This method relies on the ssDNA recombineering protocols developed for Escherichia coli, and subsequent introduction and homologous recombination, of the mutated locus into the Streptomyces strain of interest.

The ssDNA recombineering protocol relies on the high levels of recombination seen using lambda-red mediated recombination with short oligonucleotides in the absence of the methyl-directed mismatch repair (MMR) system[1, 2]. An oligonucleotide carrying the desired mutation is transformed into an MMR-deficient recombineering strain that carries the Streptomyces gene on a cosmid. This recombination using the oligonucleotide occurs at such a high frequency that selection for the desired mutation is not necessary: instead, a suitable screen (such as a diagnostic PCR) can be used to identify the recombinants.

Once the mutant allele(s) have been generated in E. coli, you can introduce the unmarked mutations into a Streptomyces strain of interest using intergeneric conjugation. Once a double cross-over has occurred, exconjugants will have either the wild-type or the mutant allele (in theory, if the mutated gene is near the centre of the cosmid, ~50% exconjugants should have the wild-type and ~50% should have the mutant allele). This process is essentially "scarless" genome editing as the resulting strains do not have any antibiotic resistance markers, or any other changes apart from the desired mutation(s).

For a comprehensive guide to ssDNA recombineering in E. coli, see the helpful guides and protocols published by the Court lab. For a guide to the Streptomyces "Redirect" method, see the helpful guides and protocols available on StrepDB.[3]

Figure 1. Illustration of two key steps in ssDNA recombineering in Streptomyces. Left, ssDNA recombineering in E. coli (Stage 2). A MMR-deficient strain of E. coli carrying the Streptomyces gene of interest, is transformed with a long oligonucleotide containing the desired mutation. Lambda-red mediated recombination occurs, generating the desired mutant allele at high frequency. Right, double cross-over in the Streptomyces strain of interest (Stage 4). The mutant allele generated in stage 2 is introduced into the chosen Streptomyces strain by intergeneric conjugation. After a double crossover occurs, the antibiotic resistance gene encoded on the cosmid is lost, and usually ~50% of the exconjugants should have the mutant allele.

Uses

  • Engineering single nucleotide changes at the native chromosomal locus
    • Amino acid changes, i.e. to study the function(s) of a particular amino acid
    • Nonsense mutations
  • Engineering small deletions/insertions (~20-30nt can be inserted[2]
  • Useful when working with essential genes that cannot be deleted using the standard "Redirect" method[4], or if the standard "Redirect" method may have polar effects on downstream genes

Organisms

This protocol has been confirmed to work for the following organisms:

Workflow Overview

Stage 1. Mutant design

Stage 2. ssDNA recombineering in E. coli

Stage 3. Identify and isolate successful recombinants. Confirm correct recombination event.

Stage 4. Introduce mutant allele(s) into your Streptomyces strains of interest.

Materials Needed

  • E. coli strains:
    • A suitable recombineering strain, such as HME68 (deficient in MMR and capable of inducible lambda red recombinase expression) - see Court lab strain list
    • DH5α or another strain suitable for cloning
    • ET12567/pUZ8002
  • Your Streptomyces strain(s) of choice
  • Oligonucleotides for introducing your desired mutation(s), screening for the mutant allele(s), and amplifying and sequencing the allele(s)


Detailed Protocols

Stage 1: Mutant design

Identify desired mutation and design suitable oligonucleotides to create this mutation. Design a suitable screen that will allow you to distinguish between wild-type and recombinant alleles. Design primers that will allow you to sequence the allele.

Step 1. in silico design of desired mutation(s)

Materials needed:

  • Sequence of the gene(s) you wish to mutate
  • DNA editing software, NEBCutter, EXPASy translate, or similar
  • Codon usage chart for your organism


Instructions:

Design suitable oligonucleotides to create your mutation(s)

  1. Identify the point mutation(s) that you want to introduce onto the chromosome. From the desired amino acid change, work backwards to identify the DNA sequence that will encode it.
  2. You will want to pay attention to codon usage (I try to keep the same relative frequency of codon usage as the wild-type codon, if possible - i.e. a frequently used codon should be replaced by another frequently used codon).
  3. Your recombineering oligo will need to be about 70bp long, with the mutation in the center.
  4. Once you have designed your recombineering oligo, take its reverse complement. (Oligos 1 and 1' in Figure 2). The oligo corresponding to the lagging strand will be more efficient for recombineering, but if you don't know which strand is the lagging strand – usually the case for our cosmids – order oligos corresponding to both strands. If designing multiple changes for the same cosmid, it may be best to first determine for one such change, which is the most efficient oligo, and then use this sense oligo for all subsequent changes.)
Figure 2. Oligonucleotide design for ssDNA recombineering. Oligo 1 (and 1') are the two long (~70nt) recombineering oligos used to introduce the desired change(s) into your gene of interest (these change(s) should be near the middle of the oligo.) Oligos A and B are shorter (~20nt) oligos used to amplify the gene for diagnostic restriction digest and sequencing.


Design a suitable screen that will allow you to distinguish between wild-type and recombinant alleles. There are two basic approaches: diagnostic restriction digest and mismatch PCR (Figure 3).

  1. First, determine whether you can use a diagnostic restriction digest. You want to determine whether there are any restriction sites that are present in your mutant allele, but absent in the wild-type.
    1. Take ~500bp on either side of the mutation and copy it into a file (for both the wild-type and mutant alleles).
    2. Use NEBCutter or a similar tool to look for restriction fragment polymorphisms. (You can do this first with the 70bp wild-type sequence/mutant oligo, to simplify the restriction map, and make it easier to see the introduction of a new restriction site. Then, you should use NEBcutter with the entire ~500bp sequence, to make sure that your restriction site is unique in the amplified sequence, so that mutant allele will be easily identified by PCR/restriction digest on a gel.)
    3. If there are no suitable diagnostic restriction digests to distinguish between wild-type and mutant alleles, go back to step 1 and try using different codons for your desired amino acid change.
  2. If none of the codon changes change a restriction site, try designing PCR primers for a diagnostic mis-match PCR – this usually works if you have at least 2-3 base pairs mutated, but can be a bit fiddly in terms of determining the right PCR conditions for a successful diagnostic PCR.
Figure 3. Diagnostic restriction digests and mismatch PCRs to identify nt changes introduced by ssDNA recombineering. Option 1 (diagnostic restriction digests, top). The desired nucleotide change(s) in your gene also introduces a restriction site. The gene can be amplified by PCR using flanking primers (usually the same as oligos A and B in Figure 2), and then digested with the restriction enzyme. The digest is analysed by gel electrophoresis. Option 2 (mismatch PCR, bottom). The desired nucleotide changes are used to design primers for a mismatch PCR. The 3' end of the mismatch oligonucleotide anneals to the mutant allele, but not the wild-type, and therefore a PCR product can only be generated if the mutant allele is present.


Order the oligos you will need:

  • Both recombineering oligos (oligo 1 and oligo 1')
  • Flanking primers for diagnostic PCR/digest and sequencing (oligos A and B)
  • Diagnostic mismatch PCR primers, if needed
  • Oligo100, if needed (see below)

Step 2. cosmid/plasmid selection

Identify a suitable cosmid or plasmid carrying the Streptomyces DNA that you wish to mutate.

  1. If working with S. coelicolor or S. venezuelae, use StrepDB to identify which cosmid(s) contain your gene of interest.
    1. If your organism of interest does not have a cosmid library, you can clone the gene and flanking sequences into an appropriate vector and use this for ssDNA recombineering. You want at least 1kb either side of your gene of interest (more is better) - the frequency with which you will observe recombination from your cosmid/plasmid onto the chromosome is dependent on the length of the sequence.
  2. If you have a choice between several different cosmids, select the one where your gene is closest to the centre of the cosmid.
  3. Check your cosmid for the sequence of Oligo 100, 5'-AAGTCGCGGTCGGAACCGTATTGCAGCAGCTTTATCATCTGCCGCTGGACGGCGCACAAATCGCGCTTAA-3' (Constantino 2003) – if there is not enough homology for the oligo to recombine with your cosmid, you can use this as a control later on.

Stage 2: ssDNA-recombineering in E. coli

Step 3. Transform the recombineering strain with the cosmid/plasmid

E. coli strain HME68 using an appropriate method (usually electroporation).

Step 4. ssDNA recombineering

Perform ssDNA-recombineering to introduce your desired mutation(s) into your cosmid/plasmid.

Step 5. Screen for successful recombinants

and purify the cosmid/plasmid by miniprep.


Stage 3: Identify and isolate successful recombinants. Confirm correct recombination event.

Step 6. Transform DH5a with your recombineered cosmid/plasmid

At this point, the miniprep will contain a mixed population of recombinant/wild-type cosmids, and you will need to isolate the cosmids that carry the mutant allele. To do this, transform recombinant cosmid/plasmids into DH5α, and screen again for recombinant cosmids.

Purify your recombinant cosmid/plasmid by miniprep. (These minipreps should now contain a pure population with only the recombinant (mutant) cosmid/plasmid.)

Step 7. Confirm the sequence of your gene/DNA sequence of interest

amplify it by PCR and use Sanger sequencing.


Stage 4. Introduce mutant allele(s) into your Streptomyces strains of interest.

Step 8. Transform ET12567/pUZ8002 with the mutant cosmid/plasmid.

Many Streptomyces strains contain a methyl-sensing restriction system therefore disrupted cosmids must initially be passaged through a non-methylating E. coli strain

Step 9. Conjugation into Streptomyces

Use your ET12567/pUZ8002,cosmid strain to conjugate your mutant allele into your desired Streptomyces strain, and select for ex-conjugants.

Restreak ex-conjugants several times, which will allow the wild-type/mutant alleles to assort into single copy such that you have exconjugants with either the wild-type or the mutant allele.

Step 10. Identify mutant exconjugants.

Screen for exconjugants carrying the mutant allele, and confirm the correct sequence (and absence of the wild-type sequence) by PCR amplification of the gene and Sanger sequencing.

References

[1] Costantino, N., & Court, D. L. (2003). Enhanced levels of lambda Red-mediated recombinants in mismatch repair mutants. Proceedings of the National Academy of Sciences of the United States of America, 100(26), 15748–15753. doi:10.1073/pnas.2434959100

[2]Sawitzke, J.A., Costantino, N., Li, X., Thomason, L.C., Bubunenko, M., Court, C., & Court, D.L. (2011). Probing Cellular Processes with Oligo-Mediated Recombination and Using the Knowledge Gained to Optimize Recombineering, Journal of Molecular Biology, 407(1), 45-59.

[3] Gust B., Challis G.L., Fowler K., Kieser T., Chater K.F.. PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc Natl Acad Sci U S A. 2003;100(4):1541‐1546. doi:10.1073/pnas.0337542100

[4]Feeney, M.A., Chandra, G., Findlay, K.C., Paget, M.S.B., & Buttner, M.J. (2017). Translational Control of the SigR-Directed Oxidative Stress Response in Streptomyces via IF3-Mediated Repression of a Noncanonical GTC Start Codon. mBio, 8(3) e00815-17; DOI: 10.1128/mBio.00815-17

Protocol developed & written by Dr. Morgan Feeney, John Innes Centre, based on the Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect") and the Court lab protocols for ssDNA recombineering.