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Nucleic Acids Research Advance Access originally published online on September 6, 2008
Nucleic Acids Research 2008 36(18):5736-5749; doi:10.1093/nar/gkn526
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Nucleic Acids Research, 2008, Vol. 36, No. 18 5736-5749
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genome integrity, repair and replication

Editing of misaligned 3'-termini by an intrinsic 3'–5' exonuclease activity residing in the PHP domain of a family X DNA polymerase

Benito Baños, José M. Lázaro, Laurentino Villar, Margarita Salas and Miguel de Vega*

Instituto de Biología Molecular ‘Eladio Viñuela’ (CSIC), Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), C/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain

*To whom correspondence should be addressed. Tel: +34 911964463; Fax: +34 911964420; Email: mdevega{at}cbm.uam.es

Correspondence may also be addressed to Margarita Salas. Tel: +34 911964675/4402; Fax: +34 911964677; Email: msalas{at}cbm.uam.es

Received July 11, 2008. Revised July 31, 2008. Accepted July 31, 2008.

Bacillus subtilis gene yshC encodes a family X DNA polymerase (PolXBs), whose biochemical features suggest that it plays a role during DNA repair processes. Here, we show that, in addition to the polymerization activity, PolXBs possesses an intrinsic 3'–5' exonuclease activity specialized in resecting unannealed 3'-termini in a gapped DNA substrate. Biochemical analysis of a PolXBs deletion mutant lacking the C-terminal polymerase histidinol phosphatase (PHP) domain, present in most of the bacterial/archaeal PolXs, as well as of this separately expressed protein region, allow us to state that the 3'–5' exonuclease activity of PolXBs resides in its PHP domain. Furthermore, site-directed mutagenesis of PolXBs His339 and His341 residues, evolutionary conserved in the PHP superfamily members, demonstrated that the predicted metal binding site is directly involved in catalysis of the exonucleolytic reaction. The implications of the unannealed 3'-termini resection by the 3'–5' exonuclease activity of PolXBs in the DNA repair context are discussed.


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