Molecular biology: A fix for RNA.
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AlkB Homolog 1, Histone H2a Dioxygenase↗
Biomedical subjects
Leona D Samson
Publications and source records attributed to Leona D Samson.
AlkB mystery solved: oxidative demethylation of N1-methyladenine and N3-methylcytosine adducts by a direct reversal mechanism.
All organisms have multiple DNA repair pathways to protect against alkylation-induced mutation and cell death. For nearly two decades, we have known that the Escherichia coli alkB gene product protects against cell killing by S(N)2-alkylating agents, probably through DNA repair. Despite numerous attempts, a specific DNA repair activity could not be assigned to AlkB. Now, a breakthrough in biology and biochemistry, coupled with the discovery of an in silico protein structure, has uncovered a novel direct reversal DNA repair mechanism that is catalyzed by AlkB, namely the oxidative demethylation of N1-methyladenine or N3-methylcytosine DNA lesions. This reaction occurs on both single- and double-stranded DNA, and requires AlkB-bound non-heme Fe(2+), O(2) and alpha-ketogluterate to oxidize the offending methyl group. This is followed by the release of succinate, CO(2) and formaldehyde, and the restoration of undamaged A or C in DNA.
Adenine↗
The adaptive imbalance in base excision-repair enzymes generates microsatellite instability in chronic inflammation.
Chronic infection and associated inflammation are key contributors to human carcinogenesis. Ulcerative colitis (UC) is an oxyradical overload disease and is characterized by free radical stress and colon cancer proneness. Here we examined tissues from noncancerous colons of ulcerative colitis patients to determine (a) the activity of two base excision-repair enzymes, AAG, the major 3-methyladenine DNA glycosylase, and APE1, the major apurinic site endonuclease; and (b) the prevalence of microsatellite instability (MSI). AAG and APE1 were significantly increased in UC colon epithelium undergoing elevated inflammation and MSI was positively correlated with their imbalanced enzymatic activities. These latter results were supported by mechanistic studies using yeast and human cell models in which overexpression of AAG and/or APE1 was associated with frameshift mutations and MSI. Our results are consistent with the hypothesis that the adaptive and imbalanced increase in AAG and APE1 is a novel mechanism contributing to MSI in patients with UC and may extend to chronic inflammatory or other diseases with MSI of unknown etiology.
Antigens, CD↗
On the 50th anniversary of solving the structure of DNA.
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DNA↗
Mutations associated with base excision repair deficiency and methylation-induced genotoxic stress.
The long-term effect of exposure to DNA alkylating agents is entwined with the cell's genetic capacity for DNA repair and appropriate DNA damage responses. A unique combination of environmental exposure and deficiency in these responses can lead to genomic instability; this "gene-environment interaction" paradigm is a theme for research on chronic disease etiology. In the present study, we used mouse embryonic fibroblasts with a gene deletion in the base excision repair (BER) enzymes DNA beta-polymerase (beta-pol) and alkyladenine DNA glycosylase (AAG), along with exposure to methyl methanesulfonate (MMS) to study mutagenesis as a function of a particular gene-environment interaction. The beta-pol null cells, defective in BER, exhibit a modest increase in spontaneous mutagenesis compared with wild-type cells. MMS exposure increases mutant frequency in beta-pol null cells, but not in isogenic wild-type cells; UV light exposure or N-methyl-N'-nitro-N-nitrosoguanidine exposure increases mutant frequency similarly in both cell lines. The MMS-induced increase in mutant frequency in beta-pol null cells appears to be caused by DNA lesions that are AAG substrates, because overexpression of AAG in beta-pol null cells eliminates the effect. In contrast, beta-pol/AAG double null cells are slightly more mutable than the beta-pol null cells after MMS exposure. These results illustrate that BER plays a role in protecting mouse embryonic fibroblast cells against methylation-induced mutations and characterize the effect of a particular combination of BER gene defect and environmental exposure.
Alkylating Agents↗
3-Methyladenine DNA glycosylase-deficient Aag null mice display unexpected bone marrow alkylation resistance.
Most cells deficient in 3-methyladenine (3MeA) DNA glycosylase become sensitive to the lethal and clastogenic effects of alkylating agents. Surprisingly, myeloid progenitor bone marrow (BM) cells derived from Aag -/- mice were more resistant than those from wild-type mice to the cytotoxic effects of several alkylating agents. Moreover, an alkylation-resistant phenotype was observed in vivo using the BM micronucleus assay as a measure of chromosome damage. Flow cytometry indicated that in vivo alkylation resistance in Aag null BM cells may be restricted to cells of the myeloid lineage. These results show that in particular cell types, the initiation of base excision repair is more lethal to the cell than leaving the damaged bases unrepaired by Aag.
Alkylating Agents↗
Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping.
We have generated a genomic phenotyping database identifying hundreds of Saccharomyces cerevisiae genes important for viable cellular recovery after mutagen exposure. Systematic phenotyping of 1,615 gene deletion strains produced distinctive signatures for each of four mutagens. Integration of the phenotyping database with mutagen-induced transcriptional profiling data demonstrated that being transcriptionally responsive to a mutagen does not predict whether or not a gene contributes to recovery from exposure to that mutagen. Computational integration of the database with 4,025 interacting proteins, comprising the yeast interactome, identified several multiprotein networks important for damage recovery. Some networks were associated with DNA metabolism and cell cycle control functions, but most were associated with unexpected functions such as cytoskeleton remodeling, chromatin remodeling, protein, RNA, and lipid metabolism. Hence, a plethora of responses other than the DNA damage response is important for recovery. These network mapping results demonstrate how systematic phenotypic assays may be linked directly to underlying molecular mechanisms.
Cell Division↗
Network responses to DNA damaging agents.
Global transcriptional profiling and large scale phenotypic studies have shown that eukaryotic cells mount a robust and complex response to damage. Further, systems biology approaches have employed powerful analytical methods to integrate global data sets with regulatory sequences, protein-DNA and protein-protein interactions, which have led to the identification of large networked responses to damage. A number of groups have shown that damage responsive networks embrace groups of highly connected genes and proteins and have illustrated that multiple interconnected cellular pathways respond to damage and moreover, dictate viability post damage. This review highlights some of the global studies that examine cellular responses to damage, and proposes that we should be moving from pathways to networks, in order to gain better insight into cellular defense mechanisms.
Animals↗