Melanie D. Ohi, Ph.D.
Vanderbilt University Medical Center
465 21st Ave So, 3160-A MRB 3
Nashville, TN 37232-8240
Studying the structure and function of macromolecular machines
Proteins carry out most cellular processes as members of dynamic multi-protein assemblies. Although progress has been made cataloging the constituents of specific complexes, we have only limited knowledge of how proteins assemble into macromolecular machines and how these machines perform their cellular functions. We are using yeast genetics, biochemistry and single particle cryo-electron microscopy (EM) to explore the structural and functional organization of complexes involved in pre-mRNA splicing and complexes involved in the protein ubiquitination pathway.
Single Particle Cryo-Electron Microscopy
Single particle cryo-EM is a powerful technique for determining the structures of large, dynamic complexes that are too difficult to crystallize. In this structural approach, purified complexes are applied to grids covered with holey carbon film and quickly frozen by plunging the grids into liquid ethane. The rapid freezing prevents water from forming ice crystals and embeds the molecules in a layer of vitrified (or amorphous) ice preserving the specimen in a near-native environment. Images of the preserved particles are taken using an electron microscope. Digital image processing methods are then used to produce 3D models from the images of complex particles trapped in vitrified ice.
Although the human genome contains ~25,000 genes, it is estimated that we make over 90,000 proteins. The disparity between our genome and our proteome can be explained by the activity of the spliceosome, a large macromolecular machine composed of RNA and protein components. This complex catalyzes the excision of non-coding introns from a pre-messenger RNA (pre-mRNA) to create a mature message (mRNA). Although the composition of the spliceosome is known, it remains a mystery how this dynamic machine functions. To understand spliceosome function and regulation it will be essential to develop three-dimensional (3D) pictures of how the numerous spliceosomal proteins and RNA components organize into one machine. A number of projects in the lab focus on the functional and structural characterization of stable spliceosomal complexes isolated from the fission yeast S. pombe.
Pore Forming Toxins
There are a number of projects in the lab that focus on studying the structure and function of pore forming bacterial toxins. We work with a multidisciplinary team of researchers to understand how these toxins function as both soluble and membrane inserted proteins, with the main goal of gaining a mechanistic understanding of how these toxins contribute to pathogenesis.
- McLean, JR, Chaix, D, Ohi, MD, Gould, KL State of the APC/C: organization, function, and structure. Crit Rev Biochem Mol Biol, 46(2), 118-36, 2011.
- Archuleta, TL, Du, Y, English, CA, Lory, S, Lesser, C, Ohi, MD, Ohi, R, Spiller, BW The Chlamydia effector, chlamydial outer protein N CopN), sequesters tubulin and prevents microtubule assembly. J Biol Chem, 2011.
- Roberts-Galbraith, RH, Ohi, MD, Ballif, BA, Chen, JS, McLeod, I, McDonald, WH, Gygi, SP, Yates, JR, Gould, KL Dephosphorylation of F-BAR protein Cdc15 modulates its conformation and stimulates its scaffolding activity at the cell division site. Mol Cell, 39(1), 86-99, 2010.
- GonzÃ¡lez-Rivera, C, Gangwer, KA, McClain, MS, Eli, IM, Chambers, MG, Ohi, MD, Lacy, DB, Cover, TL Reconstitution of Helicobacter pylori VacA toxin from purified components. Biochemistry, 49(27), 5743-52, 2010.
- Pruitt, RN, Chambers, MG, Ng, KK, Ohi, MD, Lacy, DB Structural organization of the functional domains of Clostridium difficile toxins A and B. Proc Natl Acad Sci U S A, 2010.
- Vander Kooi, CW, Ren, L, Xu, P, Ohi, MD, Gould, KL, Chazin, WJ The Prp19 WD40 domain contains a conserved protein interaction region essential for its function. Structure, 18(5), 584-93, 2010.
- Huang, DT, Hunt, HW, Zhuang, M, Ohi, MD, Holton, JM, Schulman, BA Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity. Nature, 445(7126), 394-8, 2007.
- Ohi, MD, Ren, L, Wall, JS, Gould, KL, Walz, T Structural characterization of the fission yeast U5.U2/U6 spliceosome complex. Proc Natl Acad Sci U S A, 104(9), 3195-200, 2007.
- Ohi, MD, Feoktistova, A, Ren, L, Yip, C, Cheng, Y, Chen, JS, Yoon, HJ, Wall, JS, Huang, Z, Penczek, PA, Gould, KL, Walz, T Structural organization of the anaphase-promoting complex bound to the mitotic activator Slp1. Mol Cell, 28(5), 871-85, 2007.
- Crampton, D.J., Ohi, M.D., Qimron,E., Lee,S.J., Walz, T., and Richardson, C. "Oligomeric states of bacteriophage T7 gene 4 primase/helicase." Journal of Molecular Biology, 360667-677, 2006.
- Vander Kooi, CW, Ohi, MD, Rosenberg, JA, Oldham, ML, Newcomer, ME, Gould, KL, Chazin, WJ The Prp19 U-box crystal structure suggests a common dimeric architecture for a class of oligomeric E3 ubiquitin ligases. Biochemistry, 45(1), 121-30, 2006.
- Ohi, MD, Vander Kooi, CW, Rosenberg, JA, Ren, L, Hirsch, JP, Chazin, WJ, Walz, T, Gould, KL Structural and functional analysis of essential pre-mRNA splicing factor Prp19p. Mol Cell Biol, 25(1), 451-60, 2005.
- Ohi, M.D., Li, Y., Cheng, Y. and Walz, T. "Negative staining and image classification-powerful tools in modern electron microscopy." Biol. Proc. Online, 6(1), 23-34, 2004.
- Wilkinson, CR, Dittmar, GA, Ohi, MD, Uetz, P, Jones, N, Finley, D Ubiquitin-like protein Hub1 is required for pre-mRNA splicing and localization of an essential splicing factor in fission yeast. Curr Biol, 14(24), 2283-8, 2004.
- Ohi, MD, Vander Kooi, CW, Rosenberg, JA, Chazin, WJ, Gould, KL Structural insights into the U-box, a domain associated with multi-ubiquitination. Nat Struct Biol, 10(4), 250-5, 2003.
- Ohi, MD, Gould, KL Characterization of interactions among the Cef1p-Prp19p-associated splicing complex. RNA, 8(6), 798-815, 2002.
- Ohi, MD, Link, AJ, Ren, L, Jennings, JL, McDonald, WH, Gould, KL Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Mol Cell Biol, 22(7), 2011-24, 2002.
- Berry, LD, Feoktistova, A, Wright, MD, Gould, KL The schizosaccharomyces pombe dim1(+) gene interacts with the anaphase-promoting complex or cyclosome (APC/C) component lid1(+) and is required for APC/C function. Mol Cell Biol, 19(4), 2535-46, 1999.