Polynucleotide phosphorylase is implicated in homologous recombination and DNA repair in Escherichia coli

Abstract

BackgroundPolynucleotide phosphorylase (PNPase, encoded by pnp) is generally thought of as an enzyme dedicated to RNA metabolism. The pleiotropic effects of PNPase deficiency is imputed to altered processing and turnover of mRNAs and small RNAs, which in turn leads to aberrant gene expression. However, it has long since been known that this enzyme may also catalyze template-independent polymerization of dNDPs into ssDNA and the reverse phosphorolytic reaction. Recently, PNPase has been implicated in DNA recombination, repair, mutagenesis and resistance to genotoxic agents in diverse bacterial species, raising the possibility that PNPase may directly, rather than through control of gene expression, participate in these processes.ResultsIn this work we present evidence that in Escherichia coli PNPase enhances both homologous recombination upon P1 transduction and error prone DNA repair of double strand breaks induced by zeocin, a radiomimetic agent. Homologous recombination does not require PNPase phosphorolytic activity and is modulated by its RNA binding domains whereas error prone DNA repair of zeocin-induced DNA damage is dependent on PNPase catalytic activity and cannot be suppressed by overexpression of RNase II, the other major enzyme (encoded by rnb) implicated in exonucleolytic RNA degradation. Moreover, E. coli pnp mutants are more sensitive than the wild type to zeocin. This phenotype depends on PNPase phosphorolytic activity and is suppressed by rnb, thus suggesting that zeocin detoxification may largely depend on RNA turnover.ConclusionsOur data suggest that PNPase may participate both directly and indirectly through regulation of gene expression to several aspects of DNA metabolism such as recombination, DNA repair and resistance to genotoxic agents.

Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase

“…In vitro and presence of Mn 2+ , the bacterial PNPases can catalyze both DNA phosphorolysis and synthesis of DNA from dNDPs [74][75][76][77]. Consistent with this activity, PNPases of both Gram-negative and Gram-positive bacteria have been implicated in DNA recombination, repair, and mutagenesis [77][78][79][80].…”

“…In vitro and presence of Mn 2+ , the bacterial PNPases can catalyze both DNA phosphorolysis and synthesis of DNA from dNDPs [74][75][76][77]. Consistent with this activity, PNPases of both Gram-negative and Gram-positive bacteria have been implicated in DNA recombination, repair, and mutagenesis [77][78][79][80]. Whether DNA and dNDPs may be substrates also for hPNPase and, if so, what the in vivo relevance of such activity may be on the maintenance of mtDNA are unexplored issues.…”

Bacterial ribonucleases and their roles in RNA metabolism

“…Since PNPase plays a role in so many RNA metabolic processes, it is not surprising that its absence affects cells in many ways leading to a multiplicity of phenotypes. For example, bacterial cells lacking PNPase are affected in cell motility and exhibit increased biofilm formation (Carzaniga et al 2012; Pobre and Arraiano 2015); they display increased sensitivity to antibiotics (McMurry and Levy 1987); they exhibit growth defects at low temperatures (Hossain and Deutscher 2016); they are unable to maintain control of cysteine homeostasis (Tseng et al 2015); they are more sensitive to oxidative stress (Wu et al 2009); and they are affected in DNA recombination and repair (Carzaniga et al 2017).…”

Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157

“…Polyribonucleotide nucleotidyltransferases are also known as polynucleotide phosphorylases (PNPases) and are widely conserved in all bacteria. PNPases perform core functions in the cell by regulating homologous recombination and mismatch repair ( 24 ); this could be essential for the packaging and generation of new phage progeny and the DNA metabolism involved.…”