The efforts in my laboratory focus on two very different areas of research: 1) Human DNA repair processes as they relate to cancer, immunity, and aging, and 2) Microbial extremeophiles and their application to bioenergy and global carbon cycling. These disparate projects each deal with a major problem facing modern science. Our efforts are directed at contributing and impacting these important social and scientific topics. (More at our Lab Website.)
Immunity, DNA Repair and Cancer. It may not be immediately apparent how the areas of DNA repair, immunity, and cancer are related. In our laboratory we have come to theses seemingly different topics by studying the processes of human DNA repair. As it turns out, the enzymes and pathways essential for repairing DNA are also essential for immunity and this same set of cellular processes impact both cancer development and cancer treatments. We focus much of our effort on the biochemical capabilities and cellular functions of key enzymes that intersect at these processes. Our work is focused on the particular pathway that mammalian cells use to repair DNA double-strand breaks, the non-homologous end joining (NHEJ) pathway of repair. The proteins essential for NHEJ are also required for a specific genetic recombinational event occuring in pre-B and pre-T cells that gives rise to immunodiversity and is essential for B and T cell maturation. This process is called V(D)J recombination and individuals defective in gene products needed for this recombination are afflicted with both severe combined immunodeficiency (SCID) and are hyper-sensitive to radiation and chemotherapies. Mutations in the Artemis gene cause a radiation sensitive form of SCID, which poses particular challenges to treatment. (More on Immunity and DNA-repair.)
Human Aging. We were led into this area of work by our DNA repair studies when we observed a functional interaction between the WRN protein and the DNA-dependent protein kinase (Yannone et. al 2005). The WRN protein is a multifunctional enzyme encoding helicase, nuclease and annealing activities in human cells. Individuals having mutations disrupting the function of this protein are normal children through puberty, but in early adulthood exhibit accelerated onset of many aging pathologies. Our efforts are broadly aimed at understanding the molecular events underlying the set of pathologies we ascribe to aging, with particular focus on the function of WRN protein. We have primarily taken a structure-function approach to this problem, and solved the atomic-resolution structure of the human WRN nuclease domain, and more recently identified a part of the protein that is responsible for WRN assembling into multimers. By understanding how and what the WRN enzyme does, we hope to better understand the cellular processes and the biochemical reactions that influence the aging process in humans. (More on Aging.)
Bioenergy and Climate Change. Our involvement in this collaborative project springs from my work as a graduate student at UC Irvine on metallo-proteins within the soil bacterium Azotobacter vinelandii. There we endeavored to transfer the nitrogen fixing capacity of these microbes into platnts to develop self-fertilizing crops for growth in poor soils. These efforts are ongoing in many laboratories, however the complexity of these systems has thus far precluded success in this central goal. In our current work on extremophiles, we endeavor to exploit the biochemistry of these extreme microbes to facilitate hybrid biological/chemical process to assist in meeting energy needs in carbon-neutral or carbon-negative processes. While there are many possible applications for this work, we are currently funded to do "foundational science" (i.e. basic research) necessary to rapidly identify and exploit novel biological activities to energy applications. We are establishing model systems and molecular tools to exploit biological activities in line with Department of Energy missions to address energy and climate issues facing the country and world. (More on Extremophiles.)
Microbial metalloproteomes are largely uncharacterized.
Cvetkovic A, Menon AL, Thorgersen MP, Scott JW, Poole FL 2nd, Jenney FE Jr, Lancaster WA, Praissman JL, Shanmukh S, Vaccaro BJ, Trauger SA, Kalisiak E, Apon JV, Siuzdak G, Yannone SM, Tainer JA, Adams MW. Nature. 2010 Aug 5;466(7307):779-82.
Identification of a coiled coil in werner syndrome protein that facilitates multimerization and promotes exonuclease processivity.
Perry JJ, Asaithamby A, Barnebey A, Kiamanesch F, Chen DJ, Han S, Tainer JA, Yannone SM. J Biol Chem. 2010 Aug 13;285(33):25699-707.
A nanostructure-initiator mass spectrometry-based enzyme activity assay.
Northen TR, Lee JC, Hoang L, Raymond J, Hwang DR, Yannone SM, Wong CH, Siuzdak G. Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3678-83. Epub 2008 Mar 4.
Processing of 3'-phosphoglycolate-terminated DNA double strand breaks by Artemis nuclease.
Povirk LF, Zhou T, Zhou R, Cowan MJ, Yannone SM. J Biol Chem. 2007 Feb 9;282(6):3547-58.
(More of our publications.)