TheEscherichia coliprotein YjjG is a house-cleaning nucleotidasein vivo

Abstract

House-cleaning enzymes protect cells from the adverse effects of noncanonical metabolic chemical compounds. The Escherichia coli nucleotide phosphatase YjjG (B4374, JW4336) functions as a house-cleaning phosphatase in vivo. YjjG protects the cell against noncanonical pyrimidine derivatives such as 5-fluoro-2'-deoxyuridine (5-FdUridine), 5-fluorouridine, 5-fluoroorotic acid (5-FOA), 5-fluorouracil, and 5-aza-2'-deoxycytidine. YjjG prevents the incorporation of potentially mutagenic nucleotides into DNA as shown for 5-bromo-2'-deoxyuridine (BrdU). Its enzymatic activity in vitro towards noncanonical 5-fluoro-2'-deoxyuridine monophosphate (5-FdUMP) is higher than towards canonical thymidine monophosphate (dTMP). The closest homolog in humans, HDHD4, does not show a protective effect against noncanonical nucleotides, excluding an involvement of HDHD4 in resistance against noncanonical nucleotides used for cancer chemotherapy. The substrate spectrum of YjjG suggests that its in vivo substrates are noncanonical pyrimidine derivatives, which might also include oxidized nucleobases such as 5-formyluracil and 5-hydroxyuracil.

Markers of fitness in a successful enzyme superfamily

“…The human deoxyribonucleotidases(11), which function to balance dNTP pools and to prevent dNTP accumulation, are cited as examples of HADSF phosphatase “regulators”. The HADSF phosphatase housekeepers are used for specific repair of damaged nucleic acids (e.g., removal of the 3′ phosphate at DNA strand breaks(12) and proteins (e.g., removal of the phosphate from a phosphogluconated Lys(13)), but are most commonly used to rid the cell of phosphorylated metabolites whose accidental accumulation via stalled pathways, uptake from the environment, or chemical transformation can result in catabolite repression (e.g., 2-keto-3-deoxygalactonate-6-phosphate(14) and 2-deoxyglucose-6-phosphate(15) or misincorporation (e.g., of unnatural nucleotides into DNA(16). The periplasmic HAD phosphatases of Gram negative bacteria assist nutrient uptake through the removal of phosphate groups from environmental metabolites(17).…”

Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides thetaiotaomicron BT2127 Is an Inorganic Pyrophosphatase

“…The in vivo function assignment was facilitated by gene context as well as by a narrow substrate range coupled with a high k cat /K m value for the physiological substrate. In addition, gene knockout experiments have been used to show that the promiscuous phosphatases YniC(4) and YjjG(10) can function in vivo to remove toxic 2-deoxy-glucose 6-phosphate and noncanonical nucleoside-5′-monophosphates, respectively. Genetic experiments have also shown that YjjG performs in the thymidine salvage pathway as a dUMP nucleotidase(11).…”

KsgA, a 16S rRNA adenine methyltransferase, has a novel DNA glycosylase/AP lyase activity to prevent mutations in Escherichia coli

“…Therefore, E. coli must harbor other phosphatase activities for the 5-foU derivatives. Recently, Titz et al (47) reported that the E. coli protein YjjG 5 is a house-cleaning nucleotidase in vivo and 5-foU was thought to be a candidate substrate for the protein (47). Therefore, it is likely that E. coli has a similar repair enzyme system for preventing mutations due to 5-foU and Tg to the ‘GO’ system for 8-oxoG (5–9).…”