RecF pathway

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The RecF pathway, also called the RecFOR pathway, is a pathway of homologous recombination that repairs DNA in bacteria. It repairs breaks that occur on only one of DNA's two strands, known as single-strand gaps. The RecF pathway can also repair double-strand breaks in DNA when the RecBCD pathway, another pathway of homologous recombination in bacteria, is inactivated by mutations. [1] Like the RecBCD pathway, the RecF pathway requires RecA for strand invasion. The two pathways are also similar in their phases of branch migration, in which the Holliday junction slides in one direction, and resolution, in which the Holliday junctions are cleaved apart by enzymes. [2] [3]

The RecF pathway begins when RecJ, an exonuclease that cleaves single-stranded DNA in the 5 → 3′ direction, binds to the 5' end of a single-strand gap in DNA and starts moving upstream while cleaving the 5' strand. Although RecJ can function without them, single-strand binding protein (SSBP) and the RecQ helicase greatly increase how much the 5' is cut back. When present, SSBP binds to the 3' overhang remaining after RecJ finishes cutting back the 5' strand. [3] By binding to the single-stranded DNA, SSBP ensures that the 3' DNA overhang does not stick to itself through self-complementation. [4]

The RecA protein can be loaded onto the SSBP-coated 3' overhang in one of two distinct pathways, one that requires the RecFOR enzyme or one that requires the RecOR enzyme. [5] In the RecFOR pathway, the RecFR complex binds where the single-strand DNA of the 3' meets the double-strand DNA. RecO then displaces SSBP from the ssDNA, although SSBP remains attached to RecO. RecFOR then loads RecA onto a recessed 5' end of this ssDNA-dsDNA junction. The RecR subunit in RecFR then interacts with RecO to form the RecFOR complex. In doing so, the RecR subunit helps to both detach the SSBP molecules from RecO and load molecules of the RecA protein onto the 3' overhang. [6]

The RecOR pathway of RecA loading differs from the RecFOR pathway in several respects, most notably its molecular interaction requirements and its ideal DNA substrate. [5] Unlike the RecFOR pathway, the RecOR pathway requires an interaction between RecO and the C-terminus of SSBP. The RecOR pathway also does not need a ssDNA-dsDNA junction to begin loading RecA onto the 3' overhang, whereas the RecFOR pathway typically does to work efficiently. Thus, the RecOR pathway in most conditions is more efficient than the RecFOR pathway in loading RecA. [5]

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Nuclease class of enzymes

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Stephen Charles Kowalczykowski is a Distinguished Professor of Microbiology and Molecular Genetics at the University of California at Davis. His research focuses on the biochemistry and molecular biology of DNA repair and homologous recombination. His lab combines fluorescence microscopy, optical trapping and microfluidics to manipulate and visualize single molecules of DNA and the enzymes involved in processing and repairing DNA. He calls this scientific approach, "visual biochemistry". Stephen Kowalczykowski was elected to the American Society for Arts and Science in 2005, the National Academy of Sciences in 2007 and was a Harvey Society Lecturer at Rockefeller University in 2012.

Crossover junction endodeoxyribonuclease, also known as Holliday junction resolvase, Holliday junction endonuclease, Holliday junction-cleaving endonuclease, Holliday junction-resolving endoribonuclease, crossover junction endoribonuclease, and cruciform-cutting endonuclease, is an enzyme involved in DNA repair and homologous recombination. Specifically, it performs endonucleolytic cleavage that results in single-stranded crossover between two homologous DNA molecules at the Holliday junction to produce recombinant DNA products for chromosomal segregation. This process is known as Holliday junction resolution.

Single-stranded binding protein class of proteins

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Single-strand DNA-binding protein (SSB) is a protein found in Escherichia coli bacteria, that binds to single-stranded regions of deoxyribonucleic acid (DNA). Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination, and repair. As well as stabilizing this single-stranded DNA, SSB proteins bind to and modulate the function of numerous proteins involved in all of these processes.

References

  1. ↑ Morimatsu, K; Kowalczykowski, SC (22 May 2003). "RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair". Molecular Cell. 11 (5): 1337–1347. doi:10.1016/S1097-2765(03)00188-6. PMID   12769856.
  2. ↑ Hiom, K (July 2009). "DNA Repair: Common Approaches to Fixing Double-Strand Breaks". Current Biology. 19 (13): R523–R525. doi:10.1016/j.cub.2009.06.009. PMID   19602417.
  3. 1 2 Handa, N; Morimatsu, K; Lovett, ST; Kowalczykowski, SC (15 May 2009). "Reconstitution of initial steps of dsDNA break repair by the RecF pathway of E. coli". Genes & Development. 23 (10): 1234–1245. doi:10.1101/gad.1780709. PMC   2685532 . PMID   19451222.
  4. ↑ Kowalczykowski, SC; Clow, J; Somani, R; Varghese, A (5 January 1987). "Effects of the Escherichia coli SSB protein on the binding of Escherichia coli RecA protein to single-stranded DNA. Demonstration of competitive binding and the lack of a specific protein-protein interaction". Journal of Biological Chemistry. 193 (1): 81–95. doi:10.1016/0022-2836(87)90629-2. PMID   3295259.
  5. 1 2 3 Sakai, A; Cox, MM (30 January 2009). "RecFOR and RecOR as distinct RecA loading pathways" (PDF). Journal of Biological Chemistry. 284 (5): 3264–3272. doi:10.1074/jbc.M807220200. PMC   2631980 . PMID   18986990. Archived from the original (PDF) on 17 June 2010.
  6. ↑ Inoue, H; Honda, M; Ikawa, S; Shibata, T; Mikawa, T (January 2008). "The process of displacing the single-stranded DNA-binding protein from single-stranded DNA by RecO and RecR proteins". Nucleic Acids Research. 36 (1): 94–109. doi:10.1093/nar/gkm1004. PMC   2248737 . PMID   18000001.
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