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Nucleic Acids Research Advance Access published online on May 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp314
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© Published by Oxford University Press 2009
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

Bacillus subtilis polynucleotide phosphorylase 3'-to-5' DNase activity is involved in DNA repair

Paula P. Cardenas1, Begoña Carrasco1, Humberto Sanchez1, Gintaras Deikus2, David H Bechhofer2 and Juan C Alonso1,*

1Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain and 2Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine of New York University, NY 10029, USA

*To whom correspondence should be addressed. Tel: +34 91 585 45 46; Fax: +34 91 585 45 06; Email: jcalonso{at}cnb.csic.es Present addresses: Begoña Carrasco, Area de Microbiología, Facultad de Medicina, Universidad de Oviedo, Spain Humberto Sanchez, Department of Genetics and Cell Biology, Erasmus MC, Rotterdam, The Netherlands

Received February 10, 2009. Accepted April 17, 2009.

In the presence of Mn2+, an activity in a preparation of purified Bacillus subtilis RecN degrades single-stranded (ss) DNA with a 3' -> 5' polarity. This activity is not associated with RecN itself, because RecN purified from cells lacking polynucleotide phosphorylase (PNPase) does not show the exonuclease activity. We show here that, in the presence of Mn2+ and low-level inorganic phosphate (Pi), PNPase degrades ssDNA. The limited end-processing of DNA is regulated by ATP and is inactive in the presence of Mg2+ or high-level Pi. In contrast, the RNase activity of PNPase requires Mg2+ and Pi, suggesting that PNPase degradation of RNA and ssDNA occur by mutually exclusive mechanisms. A null pnpA mutation ({Delta}pnpA) is not epistatic with {Delta}recA, but is epistatic with {Delta}recN and {Delta}ku, which by themselves are non-epistatic. The addA5, {Delta}recO, {Delta}recQ ({Delta}recJ), {Delta}recU and {Delta}recG mutations (representative of different epistatic groups), in the context of {Delta}pnpA, demonstrate gain- or loss-of-function by inactivation of repair-by-recombination, depending on acute or chronic exposure to the damaging agent and the nature of the DNA lesion. Our data suggest that PNPase is involved in various nucleic acid metabolic pathways, and its limited ssDNA exonuclease activity plays an important role in RecA-dependent and RecA-independent repair pathways.


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