A Plant Phytotoxin, Solanapyrone A, Is an Inhibitor of DNA Polymerase β and λ

Abstract

Eukaryotic cells reportedly contain three replicative DNAdirected DNA polymerases (EC 2.7.7.7) (pol ␣, ␦, and ⑀), 1 mitochondrial DNA polymerase (pol ␥), and at least nine repair types of DNA polymerase (pol ␤, ␦, ⑀, , , , , , and ) (1-8), and we have screened for natural compounds that selectively inhibit each of these eukaryotic DNA polymerases and found several inhibitors (9 -15). The purpose was to use the compounds as tools and molecular probes to distinguish DNA polymerases and to clarify their biological and in vivo functions. In this study, we found an interesting fungus-produced compound that selectively inhibits the activities of pol ␤ and pol . Interestingly, the compound was found to be a plant phytotoxin, solanapyrone A, isolated from the causal fungus of early blight disease in potato. To our knowledge, such specific natural compounds have not been reported with the exception of the pol ␤-inhibitor, prunasin, which we reported previously (13). The compound was a stronger pol ␤-inhibitor than prunasin, and no pol -inhibitors have been reported.Pol ␤ is the lowest molecular mass (39 kDa) DNA polymerase lacking such intrinsic accessory activities as 3Ј-or 5Ј-exonuclease, endonuclease, dNMP turnover, or pyrophosphorolysis (16). Pol ␤ consists of an independently folded N-terminal 8-kDa domain and C-terminal 31-kDa domain (17,18). The N-terminal domain was originally characterized as a single-stranded DNA (ssDNA)-binding domain. It was then found to possess binding specificity for the 5Ј-phosphate in gapped DNA (19 -21) and a helix-hairpin-helix motif found in several other DNA repair enzymes (22,23). Recently, Matsumoto and Kim (24) demonstrated that pol ␤ catalyzes the removal of dRP from the AP endonuclease-incised AP site via ␤-elimination as opposed to hydrolysis, and that this dRP lyase activity resides in the 8-kDa domain of pol ␤. According to recent studies (7, 25), moreover, pol ␤ is known to have another family polymerase, pol . Pol ␤ has been present in all tissues examined and is generally expressed at a low level as are a number of other so-called constitutive "house-keeping" enzymes. Although the in vivo function of the family enzyme, pol , is unclear as yet, pol appears to work in a similar manner to pol ␤ (7). As to why a plant phytotoxin is a pol ␤-family-specific inhibitor, we presently are analyzing the structure and function of pol ␤ and pol using the inhibitor from two different view-points to understand the precise role of each of the polymerases in vivo and to develop a drug design strategy for cancer chemotherapy agents. We previously reported the three-dimensional structure of pol ␤ and the N-terminal 8-kDa domain (the DNA template-binding domain) with or without long chain fatty acids to further clarify the structure and function of pol ␤ (26). Because at least pol ␤ is an essential enzyme for nucleotide excision repair (1, 2), the plant phytotoxin may lead to blockage of the DNA repair systems of rescue cancer cells under clinical radiation-therapy or chemotherapy. The plan...

The Phytotoxin Albicidin is a Novel Inhibitor of DNA Gyrase

“…This is the first example of a bacterial phytotoxin with a known molecular target in plastid DNA replication. Other phytotoxins reported to target host nucleic acid biosynthesis are targetitoxin, which inhibits plastid RNA polymerase (40), and solanapyrone, which inhibits a nuclear DNA polymerase (30). Albicidin production probably serves a dual role for X. albilineans in its niche as a wound-infecting, systemic xylem-invading sugarcane pathogen.…”

Hypersensitivity phenotypes associated with genetic and synthetic inhibitor-induced base excision repair deficiency

“…Active agents, as ascertained by inhibition of pol β DNA synthesis activity in in vitro assays, have been discovered in extracts from bacteria, marine organisms, fungi and higher plants [91,[104][105][106][107][108][109]. Many of the "pol β inhibitory" compounds (glycoglycerolipids, sulfolipids, triterpenoids, phenalenone derivatives) have been found to inhibit other polymerases as well (e.g., DNA polymerases α, γ and λ, and HIV-1 reverse transcriptase) [110][111][112][113][114][115]. The primary aim given for these studies is the possibility of inhibiting repair of DNA adducts formed after treatment with DNA-damaging anticancer agents, and thus potentiating chemotherapeutic treatments.…”

Identification of Small Molecule Synthetic Inhibitors of DNA Polymerase β by NMR Chemical Shift Mapping

“…Many of the "␤-pol inhibitory" compounds (glycoglycerolipids, sulfolipids, triterpenoids, phenalenone derivatives) have been found to inhibit other polymerases as well (e.g. DNA polymerases ␣, ␥, and and HIV-1 reverse transcriptase) (15)(16)(17)(18)(19)(20); certain triterpenoid-derivative polymerase inhibitors were more recently found to also inhibit topoisomerases (21).…”