Escherichia coli endonuclease VIII and endonuclease III are oxidative base excision repair DNA glycosylases that remove oxidized pyrimidines from DNA. The genes encoding these proteins, nei and nth, are both co-transcribed as the terminal genes in operons. nei is the terminal gene in an operon with four open reading frames that encode proteins of unknown function. This operon has two confirmed transcription initiation sites upstream of the first open reading frame and two transcript termination sites downstream of nei. nth is the terminal gene in an operon with seven open reading frames that encode proteins of unknown function. The six open reading frames immediately upstream of nth show homology to the genes rnfA, rnfB, rnfC, rnfD, rnfG and rnfE from Rhodobacter capsulatis. The rnf genes are required for nitrogen fixation in R.capsulatis and have been predicted to make up a membrane complex involved in electron transport to nitrogenase. The nth operon has transcription initiation sites upstream of the first and second open reading frames and a single transcript termination site downstream of nth. The order of genes in these operons has been conserved or partially conserved in other bacteria, although it is not known whether the genes are co-transcribed in these other organisms.

Escherichia coli formamidopyrimidine DNA glycosylase (Fpg), MutY DNA glycosylase, endonuclease VIII, and endonuclease III are oxidative base excision repair DNA glycosylases that remove oxidized bases from DNA, or an incorrect base paired with an oxidized base in the case of MutY. Since genes encoding other base excision repair proteins have been shown to be part of adaptive responses in E. coli, we wanted to determine whether the oxidative DNA glycosylase genes are induced in response to conditions that cause the type of damage their encoded proteins remove. The genes fpg, mutY, nei, and nth encode Fpg, MutY, endonuclease VIII, and endonuclease III, respectively. Multiprobe RNase protection assays were used to examine the transcript levels of these genes under conditions that induce the SoxRS, OxyR, and SOS regulons after a shift from anaerobic to aerobic growth and at different stages along the growth curve. Transcript levels for all four genes decreased as cells progressed from log-phase growth to stationary phase and increased after cells were shifted from anaerobic to aerobic growth. None of the genes were induced by hydrogen peroxide, paraquat, X rays, or conditions that induce the SOS response.In Escherichia coli, as in other prokaryotes and eukaryotes, a form of DNA repair called base excision repair removes oxidatively damaged bases from DNA (for reviews see references 14 and 60). Oxidatively damaged bases result from attack by oxygen free radicals generated during normal oxidative metabolism and by exposure to exogenous agents such as X rays and redox-generating chemicals. Base excision repair proteins called DNA glycosylases hydrolyze the N-glycosylic bond between the damaged or incorrect base and the sugar, leaving an abasic site or a strand break, depending on the type of glycosylase, which is then acted on by other proteins to complete the repair process.Formamidopyrimidine DNA glycosylase (Fpg) and MutY DNA glycosylase work together to protect cells from the mutagenic effects of the common oxidative damage 7,8-dihydro-8-oxoguanine (8-oxoG) (41). Fpg removes 8-oxoG from 8-oxoG-C pairs, giving the repair DNA polymerase a chance to put in G (10, 58). If 8-oxoG is not removed before DNA replication occurs, it can mispair with A. MutY removes A in 8-oxoG-A mispairs (41, 42). Failure of this process results in a GC 3 TA transversion. The DNA glycosylases endonuclease III (endo III) and endo VIII have overlapping substrate specificities and recognize and remove a wide range of oxidized pyrimidines. Some of these oxidized pyrimidines, such as thymine glycol, act as blocks to DNA polymerase and are lethal to cells (34, 44); oxidized cytosines such as uracil glycol, 5-hydroxyuracil, and 5-hydroxycytosine pair with A and are premutagenic, leading to GC3AT transitions (32,48,49).Using reverse transcription-PCR, we have previously shown that all four oxidative DNA glycosylase genes are transcribed as part of operons (18,19) and have determined transcription initiation and termination sites by RNase protection ...

Escherichia coli formamidopyrimidine (Fpg) DNA glycosylase and MutY DNA glycosylase are base excision repair proteins that work together to protect cells from the mutagenic effects of the commonly oxidized guanine product 7,8-dihydro-8-oxoguanine. The genes encoding these proteins, fpg and mutY, are both cotranscribed as part of complex operons. fpg is the terminal gene in an operon with the gene order radC,rpmB, rpmG, and fpg. This operon has transcription initiation sites upstream of radC, in theradC coding region, and immediately upstream offpg. There is a strong attenuator in therpmG-fpg intergenic region and three transcription termination sites downstream of fpg. There is an additional site, in the radC-rpmB intergenic region, that corresponds either to a transcription initiation site or to an RNase E or RNase III cleavage site. mutY is the first gene in an operon with the gene order mutY, yggX, mltC, andnupG. This operon has transcription initiation sites upstream of mutY, in the mutY coding region, and immediately upstream of nupG. There also appear to be attenuators in the yggX-mltC and mltC-nupGintergenic regions. The order of genes in these operons has been conserved or partially conserved only in other closely related gram-negative bacteria, although it is not known whether the genes are cotranscribed in these other organisms.