Environmental Factor, April 2011, National Institute of Environmental Health Sciences
Intramural papers of the month
By Jeffrey Stumpf and Ritu Rana
- SNPs modulate cellular stress response
- Decreasing DNA binding may reverse mutator phenotype
- Regulation of metabolic syndrome by the nuclear receptor TAK1/TR4
- Occupational hazards of agriculture
SNPs modulate cellular stress response
Researchers from the NIEHS Environmental Genomics Group have identified human single-nucleotide polymorphisms (SNPs) that change the expression of a nearby gene in response to cellular stress. Binding of the p53 tumor suppressor to a specific sequence of DNA, which activates transcription of the target genes, was altered by the SNPs.
Most of 14.5 million human SNPs likely include non-coding SNPs that affect gene expression by altering DNA binding by transcription factors. This study used a bioinformatic approach to narrow the 6538 SNPs in suggested p53 binding sites to 32 likely candidates and validated this approach with a global search using chromatin immunoprecipitation. Binding of p53 to sequences containing these SNPs was directly tested using a microsphere DNA binding assay. Finally, the researchers reported changes in gene expression in human cell lines treated with a known agonist of the p53 response, doxorubicin.
Activation of the cascade of genes under p53 control in response to DNA damaging agents is important for suppression of tumors. Changes in the intensity of the p53 response changes depending on genetic sequence, as seen in this study, may explain different susceptibilities of environmentally induced diseases such as cancer.
Citation: Bandele OJ, Wang X, Campbell MR, Pittman GS, Bell DA.(https://www.ncbi.nlm.nih.gov/pubmed/20817676) 2011. Human single-nucleotide polymorphisms alter p53 sequence-specific binding at gene regulatory elements. Nucleic Acids Res 39(1):178-189.
Decreasing DNA binding may reverse mutator phenotype
In a collaborative effort, researchers from NIEHS and the Polish Academy of Sciences reported the strongly antimutagenic impact of an amino acid replacement in the RB69 viral DNA polymerase. The results, published in the Journal of Molecular Biology, showed that the powerful mutator phenotype of one amino acid replacement (Tyr567Ala) is reversed when paired with another replacement (Ser565Gly), even though Ser565Gly by itself hardly affects fidelity.
RB69 is a bacteriophage that uses its own DNA polymerase when infecting E. coli cells. Good crystal structures of the RB69 polymerase and easily measured replication fidelity make this polymerase ideal for studying basic aspects of how polymerases prevent mutagenesis. The Ser565Gly replacement seems to work both by altering the binding of the polymerase to DNA in a way that promotes the antimutagenic action of DNA proofreading by the same or new polymerase molecule, and by rendering the DNA binding pocket more rigid, and thus more able to reject imperfect base-base mispairs.
Mutagenesis affects many aspects of human health, including genetic diseases, accumulation of drug-resistant bacteria and viruses, and precursors to cancer. Basic research in DNA replication is key to understanding the role of mutagenesis in disease and providing potential targets for pharmaceutical agents.
Citation: Trzemecka A, Jacewicz A, Carver GT, Drake JW, Bebenek A.(https://www.ncbi.nlm.nih.gov/pubmed/20950625) 2011. Reversal of a mutator activity by a nearby fidelity-neutral substitution in the RB69 DNA polymerase binding pocket. J Mol Biol 404(5):778-793.
Regulation of metabolic syndrome by the nuclear receptor TAK1/TR4
Researchers from NIEHS and the University of Pittsburgh performed a collaborative study on transforming growth factor beta-activated kinase 1 (TAK1)-deficient mice (TAK1-/-) to demonstrate that the loss of TAK1, an orphan nuclear receptor, protects mice against age- and high fat diet (HFD)-induced metabolic syndrome. The study indicated that TAK1 plays a critical role in regulating lipid and energy homeostasis and, thus, may provide a novel therapeutic target for obesity and related pathologies.
Researchers generated TAK1-/- mice to better understand the role of TAK1 in obesity and associated pathologies. Using histo- and biochemical assays, they found that TAK1-/- mice have low hepatic triglycerides and reduced lipid accumulation in adipose tissue. Microarrays of TAK1-/- mice livers revealed that the expression of several genes involved in lipid uptake and triglyceride synthesis and storage was greatly decreased. TAK1-/- mice were lean and had a higher rate of energy expenditure. Further, the study reported that TAK1-/- mice had reduced inflammatory response in white adipose tissues and were resistant to glucose intolerance and insulin insensitivity.
Altogether, the authors suggest that the TAK1-deficiency prevents TAK1-/- mice from age- and HFD-induced liver injury, obesity, and related pathologies, such as diabetes. The findings provide a new therapeutic target for obesity-linked diseases.
Citation: Kang HS, Okamoto K, Kim YS, Takeda Y, Bortner CD, Dang H, Wada T, Xie W, Yang XP, Liao G, Jetten AM. (https://www.ncbi.nlm.nih.gov/pubmed/20864514) 2011. Nuclear orphan receptor TAK1/TR4-deficient mice are protected against obesity-linked inflammation, hepatic steatosis, and insulin resistance. Diabetes 60(1):177-188.
Occupational hazards of agriculture
Although farmers have lower mortality rates when compared to the general population, NIEHS scientists found that farmers continue to be at higher risk for unintentional fatal injuries. Using mortality data from 1993 to 2007 for the Agricultural Health Study (AHS), a cohort study of pesticide applicators and their spouses in North Carolina and Iowa, the researchers found that although all-cause mortality was significantly lower than expected, there was a four-fold increase in machine-related deaths. Mortality from motor vehicle non-traffic accidents and collisions was also elevated.
The study also found that certain types of cancers are more common among farmers. Using relative standardized mortality ratios to control for the fact that farmers tend to be healthier than the general population, researchers found that the relative mortality ratios were higher for cancers such as lymphohematopoietic, melanoma, prostate, and breast cancers. There were no elevations in chronic disease mortality from non-cancer outcomes. Team members suggest that an extended follow-up could provide new insights on the occupational hazards in agricultural populations.
Citation: Waggoner JK, Kullman GJ, Henneberger PK, Umbach DM, Blair A, Alavanja MC, Kamel F, Lynch CF, Knott C, London SJ, Hines CJ, Thomas KW, Sandler DP, Lubin JH, Beane Freeman LE, Hoppin JA.(https://www.ncbi.nlm.nih.gov/pubmed/21084556) 2011. Mortality in the Agricultural Health Study, 1993-2007. Am J Epidemiol 173(1):71-83.
(Jeffrey Stumpf, Ph.D., is a postdoctoral fellow in the NIEHS Laboratory of Molecular Genetics Mitochondrial DNA Replication Group. Ritu Rana, Ph.D., is a visiting fellow in the NIEHS Laboratory of Toxicology and Pharmacology Human Metabolism Group.)