RecA-independent Single-stranded DNA Oligonucleotide-mediated Mutagenesis

Overview

Journal F1000 Biol Rep

Specialty Biology

Date 2010 Aug 17

PMID 20711416

Citations 7

Authors

Kenan C Murphy

Martin G Marinus

Affiliations

Soon will be listed here.

Abstract

The expression of Beta, the single-stranded annealing protein (SSAP) of bacteriophage lambda in Escherichia coli promotes high levels of oligonucleotide (oligo)-mediated mutagenesis and offers a quick way to create single or multiple base pair insertions, deletions, or substitutions in the bacterial chromosome. High rates of mutagenesis can be obtained by the use of mismatch repair (MMR)-resistant mismatches or MMR-deficient hosts, which allow for the isolation of unselected mutations. It has recently become clear that many bacteria can be mutagenized with oligos in the absence of any SSAP expression, albeit at a much lower frequency. Studies have shown that inactivation or inhibition of single-stranded DNA (ssDNA) exonucleases in vivo increases the rate of SSAP-independent oligo-mediated mutagenesis. These results suggest that lambda Beta, in addition to its role in annealing the oligo to ssDNA regions of the replication fork, promotes high rates of oligo-mediated mutagenesis by protecting the oligo from destruction by host ssDNA exonucleases.

Citing Articles

Recombineering in Non-Model Bacteria.

Corts A, Thomason L, Costantino N, Court D Curr Protoc. 2022; 2(12):e605.

PMID: 36546891 PMC: 9793987. DOI: 10.1002/cpz1.605.

Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics.

Fels U, Gevaert K, Van Damme P Front Microbiol. 2020; 11:548410.

PMID: 33013782 PMC: 7516269. DOI: 10.3389/fmicb.2020.548410.

DNA assembly using common laboratory bacteria: A re-emerging tool to simplify molecular cloning.

Watson J, Garcia-Nafria J J Biol Chem. 2019; 294(42):15271-15281.

PMID: 31522138 PMC: 6802500. DOI: 10.1074/jbc.REV119.009109.

Replicative DNA polymerase δ but not ε proofreads errors in Cis and in Trans.

Flood C, Rodriguez G, Bao G, Shockley A, Kow Y, Crouse G PLoS Genet. 2015; 11(3):e1005049.

PMID: 25742645 PMC: 4351087. DOI: 10.1371/journal.pgen.1005049.

Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis.

Ioerger T, OMalley T, Liao R, Guinn K, Hickey M, Mohaideen N PLoS One. 2013; 8(9):e75245.

PMID: 24086479 PMC: 3781026. DOI: 10.1371/journal.pone.0075245.

References

Datta S, Costantino N, Zhou X, Court D . Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages. Proc Natl Acad Sci U S A. 2008; 105(5):1626-31. PMC: 2234195. DOI: 10.1073/pnas.0709089105. View

Wang T . Discontinuous or semi-discontinuous DNA replication in Escherichia coli?. Bioessays. 2005; 27(6):633-6. DOI: 10.1002/bies.20233. View

Kmiec E, Holloman W . Beta protein of bacteriophage lambda promotes renaturation of DNA. J Biol Chem. 1981; 256(24):12636-9. View

Carter D, Radding C . The role of exonuclease and beta protein of phage lambda in genetic recombination. II. Substrate specificity and the mode of action of lambda exonuclease. J Biol Chem. 1971; 246(8):2502-12. View

Little J . An exonuclease induced by bacteriophage lambda. II. Nature of the enzymatic reaction. J Biol Chem. 1967; 242(4):679-86. View

Kmiec E . Targeted gene repair -- in the arena. J Clin Invest. 2003; 112(5):632-6. PMC: 182220. DOI: 10.1172/JCI19777. View

Passy S, Yu X, Li Z, Radding C, Egelman E . Rings and filaments of beta protein from bacteriophage lambda suggest a superfamily of recombination proteins. Proc Natl Acad Sci U S A. 1999; 96(8):4279-84. PMC: 16323. DOI: 10.1073/pnas.96.8.4279. View

Moerschell R, Tsunasawa S, Sherman F . Transformation of yeast with synthetic oligonucleotides. Proc Natl Acad Sci U S A. 1988; 85(2):524-8. PMC: 279583. DOI: 10.1073/pnas.85.2.524. View

Radecke S, Radecke F, Peter I, Schwarz K . Physical incorporation of a single-stranded oligodeoxynucleotide during targeted repair of a human chromosomal locus. J Gene Med. 2005; 8(2):217-28. DOI: 10.1002/jgm.828. View

10.

Onrust R, Finkelstein J, Turner J, Naktinis V, ODonnell M . Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. III. Interface between two polymerases and the clamp loader. J Biol Chem. 1995; 270(22):13366-77. DOI: 10.1074/jbc.270.22.13366. View

11.

Parekh-Olmedo H, Kmiec E . Progress and prospects: targeted gene alteration (TGA). Gene Ther. 2007; 14(24):1675-80. DOI: 10.1038/sj.gt.3303053. View

12.

Mythili E, Kumar K, Muniyappa K . Characterization of the DNA-binding domain of beta protein, a component of phage lambda red-pathway, by UV catalyzed cross-linking. Gene. 1996; 182(1-2):81-7. DOI: 10.1016/s0378-1119(96)00518-5. View

13.

Engstrom J, Suzuki T, Kmiec E . Regulation of targeted gene repair by intrinsic cellular processes. Bioessays. 2009; 31(2):159-68. DOI: 10.1002/bies.200800119. View

14.

Stukenberg P, Turner J, ODonnell M . An explanation for lagging strand replication: polymerase hopping among DNA sliding clamps. Cell. 1994; 78(5):877-87. DOI: 10.1016/s0092-8674(94)90662-9. View

15.

Grogan D, Stengel K . Recombination of synthetic oligonucleotides with prokaryotic chromosomes: substrate requirements of the Escherichia coli/lambdaRed and Sulfolobus acidocaldarius recombination systems. Mol Microbiol. 2008; 69(5):1255-65. DOI: 10.1111/j.1365-2958.2008.06356.x. View

16.

Copeland N, Jenkins N, Court D . Recombineering: a powerful new tool for mouse functional genomics. Nat Rev Genet. 2001; 2(10):769-79. DOI: 10.1038/35093556. View

17.

Court D, Sawitzke J, Thomason L . Genetic engineering using homologous recombination. Annu Rev Genet. 2002; 36:361-88. DOI: 10.1146/annurev.genet.36.061102.093104. View

18.

Li X, Costantino N, Lu L, Liu D, Watt R, Cheah K . Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli. Nucleic Acids Res. 2003; 31(22):6674-87. PMC: 275540. DOI: 10.1093/nar/gkg844. View

19.

Murphy K . The lambda Gam protein inhibits RecBCD binding to dsDNA ends. J Mol Biol. 2007; 371(1):19-24. DOI: 10.1016/j.jmb.2007.05.085. View

20.

Poteete A . Involvement of DNA replication in phage lambda Red-mediated homologous recombination. Mol Microbiol. 2008; 68(1):66-74. DOI: 10.1111/j.1365-2958.2008.06133.x. View