Name: mutagenesis and functional selection protocols for directed evolution of proteins in e. coli
Uploaded: 2011-03-16T11:00:00
Duration: 9 min 1 s
Description: Watch this Scientific Journal Video about Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli at JoVE.com

This work has been supported by K08 award CA116429-04 to MC and by a grant from the Conquer Cancer Now (CONCERN) foundation # 8501

<ol>
	<li>Camps, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modulation+of+ColE1-like+plasmid+replication+for+recombinant+gene+expression.">Modulation of ColE1-like plasmid replication for recombinant gene expression.</a> Recent Pat DNA Gene Seq. 4, 58-73 (2010).</li><li>Itoh, T., Tomizawa, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Initiation+of+replication+of+plasmid+ColE1+DNA+by+RNA+polymerase,+ribonuclease+H,+and+DNA+polymerase+I.">Initiation of replication of plasmid ColE1 DNA by RNA polymerase, ribonuclease H, and DNA polymerase I.</a> Cold Spring Harb Symp Quant Biol. 43 Pt 1, 409-417 (1979).</li><li>Polisky, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ColE1+replication+control+circuitry:+sense+from+antisense.">ColE1 replication control circuitry: sense from antisense.</a> Cell. 55, 929-932 (1988).</li><li>Camps, M., Naukkarinen, J., Johnson, B. P., Loeb, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeted+gene+evolution+in+Escherichia+coli+using+a+highly+error-prone+DNA+polymerase+I.">Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I.</a> Proc Natl Acad Sci U S A. 100, 9727-9732 (2003).</li><li>Shinkai, A., Loeb, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+mutagenesis+by+Escherichia+coli+DNA+polymerase+I.+Ile(709)+in+motif+A+functions+in+base+selection.">In vivo mutagenesis by Escherichia coli DNA polymerase I. Ile(709) in motif A functions in base selection.</a> J Biol Chem. 276, 46759-46764 (2001).</li><li>Uyemura, D., Lehman, I. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biochemical+characterization+of+mutant+forms+of+DNA+polymerase+I+from+Escherichia+coli.+I.+The+polA12+mutation.">Biochemical characterization of mutant forms of DNA polymerase I from Escherichia coli. I. The polA12 mutation.</a> J Biol Chem. 251, 4078-4084 (1976).</li><li>Sedgwick, B., Robins, P., Lindahl, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+removal+of+alkylation+damage+from+DNA+by+AlkB+and+related+DNA+dioxygenases.">Direct removal of alkylation damage from DNA by AlkB and related DNA dioxygenases.</a> Methods Enzymol. 408, 108-120 (2006).</li><li>Aharoni, A., Gaidukov, L., Khersonsky, O., Mc, Q. G. S., Roodveldt, C., Tawfik, D. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+'evolvability'+of+promiscuous+protein+functions.">The 'evolvability' of promiscuous protein functions.</a> Nat Genet. 37, 73-76 (2005).</li><li>Elena, S. F., Lenski, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evolution+experiments+with+microorganisms:+the+dynamics+and+genetic+bases+of+adaptation.">Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation.</a> Nat Rev Genet. 4, 457-469 (2003).</li><li>Itoh, T., Tomizawa, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FoFormation+of+an+RNA+primer+for+initiation+of+replication+of+ColE1+DNA+by+ribonuclease+H.">FoFormation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H.</a> Proc Natl Acad Sci U S A. 77, 2450-2454 (1980).</li><li>Bryan, S. K., Moses, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sufficiency+of+the+Klenow+fragment+for+survival+of+polC(Ts)+pcbA1+Escherichia+coli+at+43+degrees.">Sufficiency of the Klenow fragment for survival of polC(Ts) pcbA1 Escherichia coli at 43 degrees.</a> C. J Bacteriol. 170, 456-458 (1988).</li></ol>

No conflicts of interest declared.

This article presents a mutagenesis protocol that allows the generation of large random mutant libraries without the need for cloning or PCR. This method is based on error-prone replication of a plasmid encoding a sequence of interest. In theory, mutations should be largely restricted to the 100-300 bp located immediately downstream of the RNA/DNA switch, the size of leader strand intermediate produced by Pol I 2,10. We found that under the conditions presented in this protocol, Pol I mutations occur all over the plasmid, although diminishing in frequency as the distance from the plasmid ori increases (Figure 3). This finding implies that the transition or "switch" from Pol I to Pol III during ColE1 plasmid replication is much more gradual than previously reported, at least under our experimental conditions 2, and agrees with earlier studies suggesting a functional redundancy between Pol I and Pol III 11.
Our original protocol described mutagenesis in liquid cultures (4). This protocol yields 0.41 mutations/kb for d&lt;1000, i.e. within the 1000 bp adjacent to the RNA/DNA switch (Table 1). Hypersaturation by leaving the liquid culture in the shaker for 3 days without the addition of any fresh media raises the mutation frequency to 0.70 mutations/kb but results in very poor plasmid yield (less than 1% compared to day 1; data not shown) (Table 1). Here we present a simplified protocol based on directly plating the transformation of the target plasmid on solid agar at 37 &deg;C (Figure 1). This procedure produces the largest frequency of mutation/cycle of mutagenesis (0.92 mutations/kb for d&lt;1000) and greatly facilitates iteration. Changing culture conditions to solid media also affects the mutation spectrum (Table 2). Direct plating mutagenesis reduces the marked asymmetry between complementary base pair substitutions seen in liquid culture (compare C&#8594;T vs. G&#8594;A and A&#8594;G vs. T&#8594;C). On the other hand, direct plating produced more indels (from less than 0.5% to 4%) and decreased the number of A&#8594;G mutations by 3-fold, leading to an overrepresentation of G/C mutations (74%). Overall, we believe that the greater simplicity and increased efficiency of the direct plating protocol presented here outweighs the benefits of the slightly more balanced mutation spectrum produced by liquid mutagenesis.
Within the target plasmid, the mutations generated by our method are not restricted to the desired target sequence. However, the evolution of novel biochemical activities should be dependent on mutations within the target gene, as it represents a qualitative rather than a quantitative change. Thus, combining our plasmid mutagenesis with screening of mutants on gradient plates capitalizes on the strengths of our system (large libraries and availability of selection) for the evolution of new biochemical properties. Other applications of random mutagenesis such as optimizing existing enzymatic activities or randomizing specific areas of a gene do require cloning following random mutagenesis. In this case, having the library in a plasmid as opposed to a PCR amplification product improves the efficiency of cloning by facilitating amplification and restriction.
In sum, we demonstrate a simple protocol to create a random mutant library for a given target gene that stands out for its simplicity and for the diversity of the libraries generated. We show how this method can be coupled with functional selections for the efficient evolution of new biochemical activities. In addition, our in vivo-generated libraries can be easily cloned, allowing site-specific mutagenesis or optimization of existing activities.

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		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
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		<tbody>
		
<tr>
<td>carbenicillin</td>
<td>&nbsp;</td>
<td>CellGro</td>
<td>46100R6</td>
<td>0.1mg/ml final</td>
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<tr>
<td>tetracycline</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>BP7640</td>
<td>0.05mg/ml final</td>
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<td>chloramphenicol</td>
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<td>Genlantis</td>
<td>M120100</td>
<td>0.03mg/ml final</td>
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<tr>
<td>LB Agar Miller</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>BP1425</td>
<td>&nbsp;</td>
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<td>LB Broth Miller</td>
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<td>Difco</td>
<td>244620</td>
<td>&nbsp;</td>
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<td>Soft Agar</td>
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<td>Difco</td>
<td>214580</td>
<td>Made in house</td>
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<td>Acridine Orange</td>
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<td>Sigma</td>
<td>A38401-1</td>
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<td>Antifoam B emulsion</td>
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<td>Sigma</td>
<td>A5757</td>
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<td>Glycerol</td>
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<td>332030025</td>
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<td>100x100x15mm sq dish</td>
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<td>Fisher</td>
<td>0875711A</td>
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<td>100mm rnd dish </td>
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<td>Fisher</td>
<td>0875712A</td>
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<td>Microscope slide 25x75x1mm</td>
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<td>Gold Seal</td>
<td>3048</td>
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<td>Electroporator 2510</td>
<td>&nbsp;</td>
<td>Eppendorf</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
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<td>Electroporator 2510</td>
<td>&nbsp;</td>
<td>Eppendorf</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
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<td>2mm gap tubes</td>
<td>&nbsp;</td>
<td>MolBioproducts</td>
<td>5520</td>
<td>&nbsp;</td>
<tr>
<td>Zippy mini prep kit</td>
<td>&nbsp;</td>
<td>Zymo </td>
<td>D4020</td>
<td>&nbsp;</td>		</tbody>
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mutagenesis and functional selection protocols for directed evolution of proteins in e. coli

The efficient generation of genetic diversity represents an invaluable molecular tool that can be used to label DNA synthesis, to create unique molecular signatures, or to evolve proteins in the laboratory. Here, we present a protocol that allows the generation of large (>1011) mutant libraries for a given target sequence. This method is based on replication of a ColE1 plasmid encoding the desired sequence by a low-fidelity variant of DNA polymerase I (LF-Pol I). The target plasmid is transformed into a mutator strain of E. coli and plated on solid media, yielding between 0.2 and 1 mutations/kb, depending on the location of the target gene. Higher mutation frequencies are achieved by iterating this process of mutagenesis. Compared to alternative methods of mutagenesis, our protocol stands out for its simplicity, as no cloning or PCR are involved. Thus, our method is ideal for mutational labeling of plasmids or other Pol I templates or to explore large sections of sequence space for the evolution of activities not present in the original target. The tight spatial control that PCR or randomized oligonucleotide-based methods offer can also be achieved through subsequent cloning of specific sections of the library. Here we provide protocols showing how to create a random mutant library and how to establish drug-based selections in E. coli to identify mutants exhibiting new biochemical activities.

Watch this Scientific Journal Video about Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli at JoVE.com

Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli

Here we demonstrate a simple protocol to create a random mutant library for a given target sequence. We show how this method, which is performed in vivo in Escherichia coli, can be coupled with functional selections to evolve new enzymatic activities.

Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli

The efficient generation of genetic diversity represents an invaluable molecular tool that can be used to label DNA synthesis, to create unique molecular ...

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