127 Lineberger, CB #7295
Our laboratory continues to focus on the use of electron microscopy (EM) to elucidate broad mechanisms of DNA protein interactions as they impinge on cancer and oncogenesis. Three areas central to cancer merit particular review: basic studies of DNA replication, studies of DNA repair and the involvement of p53 as a sensor of DNA damage and studies of the structure of human telomeres.
- Studies of DNA replication in model systems and in the oncogenic human viruses HSV and HPV. Our work on DNA replication has resulted in two publications with Charles Richardson and his laboratory that have provided firm proof of the trombone model of DNA replication, a model that has been seeking such direct proof since it was presented by Bruce Alberts 25 years ago. In a paper in J Biol Chem we demonstrated that the T7 replication system is able to replicate DNA in a coordinated manner and that trombone loops involving the lagging strand can be directly seen by EM. In a paper that just appeared in Mol Cell we show that a tiny DNA template of 70 base pairs is also replicated by the trombone mechanism, and that the tiny circle rotates within the protein machinery at 240 RPM.
- Using a combination of EM and biochemical approaches we have collaborated with Robert Lehman at Stanford to study the mechanism by which two HSV proteins, UL9 and ICP8 activate the origin of Herpes Simplex virus. Previously there had been no direct evidence that the UL9 origin binding protein could unwind the HSV origin. In a paper in EMBO J, we demonstrated that UL9 can unwind the HSV origin and in an ATP dependent manner will generate large loops of unwound DNA. In work nearing publication we have extended this finding to include studies of how the ICP8 protein facilitates the unwinding step. This is a very important area of HSV research since it has the potential to identify new drug target steps. In work with Drs. Tom Broker and Louise Chow, we have initiated studies (submitted for publication) on how the human papilloma virus E1 protein activates the origin of HPV and how this process is greatly augmented by two human heat shock proteins HSP40 and HSP70.
- Studies of DNA mismatch repair and the role of p53 protein. Our laboratory has had a longstanding interest in the mechanism by which the mismatch repair proteins identify damage in DNA. This goes back 12 years in studies of the E coli mutS protein with Paul Modrich at Duke University and our own studies of how the recA protein will recognize certain damage in DNA. A key paper was published with the Modrich laboratory in 1997 (cover of EMBO J) demonstrating that the mutHSL system identifies damage in DNA by a mechanism that involves the mutS induced formation of a loop in the DNA. The loop grows in size beginning at a mismatch in an ATP dependent manner until a signal (hemi methylated GATC) is found. This then signals the subsequent repair steps.
Eric D. Horowitz; K. Shefaet Rahman; Brian D. Bower; David J. Dismuke; Michael R. Falvo; Jack D. Griffith; Stephen C. Harvey; Aravind Asokan Biophysical and ultrastructural characterization of adeno-associated virus capsid uncoating and genome release Journal of Virology. 2013;87(6):2994-3002.
Stefanie Hartman Chen; Jody L. Plank; Smaranda Willcox; Jack D. Griffith; Tao-Shih Hsieh Improved methods for creating migratable Holliday junction substrates Nucleic Acids Research. 2013;41(5):e60.
Yoshiyuki Shibata; Pankaj Kumar; Ryan Layer; Smaranda Willcox; Jeffrey R. Gagan; Jack D. Griffith; Anindya Dutta Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues Science. 2012;335(6077):82-86. 5
Congying Wu; Sreeja B. Asokan; Matthew E. Berginski; Elizabeth M. Haynes; Norman E. Sharpless; Jack D. Griffith; Shawn M. Gomez; James E. Bear Arp2/3 is critical for lamellipodia and response to extracellular matrix cues but is dispensable for chemotaxis Cell. 2012;148(5):973-987.
Ravindra Amunugama; Yujiong He; Smaranda Willcox; Robert A. Forties; Kang-Sup Shim; Ralf Bundschuh; Yu Luo; Jack Griffith; Richard Fishel RAD51 protein ATP cap regulates nucleoprotein filament stability Journal of Biological Chemistry. 2012;287(12):8724-8736.
Xiumei Guo; Mehmet Kesimer; Gã Tolun; Xunhai Zheng; Qing Xu; Jing Lu; John K. Sheehan; Jack D. Griffith; Xiaoling Li The NAD +-dependent protein deacetylase activity of SIRT1 is regulated by its oligomeric status Scientific Reports. 2012;2.
Katarina Visacka; Ctirad Hofr; Smaranda Willcox; Ivona Necasova; Jana Pavlouskova; Regina Sepsiova; Michaela Wimmerova; Lucia Simonicova; Jozef Nosek; Jiri Fajkus; et al. Synergism of the two Myb domains of Tay1 protein results in high affinity binding to telomeres Journal of Biological Chemistry. 2012;287(38):32206-32215.
N. Özlem Arat; Jack D. Griffith Human Rap1 interacts directly with telomeric DNA and regulates TRF2 localization at the telomere Journal of Biological Chemistry. 2012;287(50):41583-41594.
Sezgin Ozgur; Blossom Damania; Jack Griffith The Kaposi's sarcoma-associated herpesvirus ORF6 DNA binding protein forms long DNA-free helical protein filaments Journal of Structural Biology. 2011;174(1):37-43.
Nathan A. Tanner; Gökhan Tolun; Joseph J. Loparo; Slobodan Jergic; Jack D. Griffith; Nicholas E. Dixon; Antoine M. Van Oijen E. coli DNA replication in the absence of free β clamps EMBO Journal. 2011;30(9):1830-1840.
Arnab Roy Chowdhury; Rahul Bakshi; Jianyang Wang; Gokben Yildirir; Beiyu Liu; Valeria Pappas-Brown; Gökhan Tolun; Jack D Griffith; Theresa A Shapiro; Robert E Jensen; et al. The killing of African trypanosomes by ethidium bromide. PLoS pathogens. 2010;6(12):e1001226.
Mehmet Kesimer; Alexander M. Makhov; Jack D. Griffith; Pedro Verdugo; John K. Sheehan Unpacking a gel-forming mucin: A view of MUC5B organization after granular release American Journal of Physiology - Lung Cellular and Molecular Physiology. 2010;298(1):L15-L22.
Jaakko L.O. Pohjoismäki; J. Bradley Holmes; Stuart R. Wood; Ming-Yao Yang; Takehiro Yasukawa; Aurelio Reyes; Laura J. Bailey; Tricia J. Cluett; Steffi Goffart; Smaranda Willcox; et al. Mammalian mitochondrial DNA replication intermediates are essentially duplex but contain extensive tracts of RNA/DNA hybrid Journal of Molecular Biology. 2010;397(5):1144-1155.
Beiyu Liu; Gokben Yildirir; Jianyang Wang; Gökhan Tolun; Jack D. Griffith; Paul T. Englund TbPIF1, a Trypanosoma brucei mitochondrial DNA helicase, is essential for kinetoplast minicircle replication Journal of Biological Chemistry. 2010;285(10):7056-7066.
Sarah A. Compton; Sezgin Özgür; Jack D. Griffith Ring-shaped Rad51 paralog protein complexes bind holliday junctions and replication forks as visualized by electron microscopy Journal of Biological Chemistry. 2010;285(18):13349-13356.
Ulrich Rass; Sarah A. Compton; Joao Matos; Martin R. Singleton; Stephen C. Y. Ip; Miguel G. Blanco; Jack D. Griffith; Stephen C. West. Mechanism of Holliday junction resolution by the human GNE1 protein. Genes and Development. 2010;24(14):1559-1569.
Tina Thorslund; Michael J. McIlwraith; Sarah A. Compton; Sergey Lekomtsev; Mark Petronczki; Jack D. Griffith; Stephen C. West The breast cancer tumor suppressor BRCA2 promotes the specific targeting of RAD51 to single-stranded DNA Nature Structural and Molecular Biology. 2010;17(10):1263-1265.
Juraj Kramara; Smaranda Willcox; Stanislava Gunisova; Slavomir Kinsky; Jozef Nosek; Jack D. Griffith; Lubomir Tomaska Tay1 protein, a novel telomere binding factor from Yarrowia lipolytica Journal of Biological Chemistry. 2010;285(49):38078-38092.
Arnab Roy Chowdhury; Rahul Bakshi; Jianyang Wang; Gokben Yildirir; Beiyu Liu; Valeria Pappas-Brown; Gökhan Tolun; Jack D. Griffith; Theresa A. Shapiro; Robert E. Jensen; et al. The killing of African trypanosomes by ethidium bromide PLoS Pathogens. 2010;6(12).