Suzanne B. Sandmeyer
Professor, Grace Beekhuis Bell Chair of Biological Chemistry, Biological Chemistry
Professor, Microbiology & Molecular Genetics
Professor, Chemical Engineering & Materials Science
|Molecular genetics and biochemistry of retrotransposons and metabolic engineering in yeast|
|Department of Biological Chemistry|
|UCI Genomics Core Facility|
|Institute for Genomics and Bioinformatics|
American Academy of Microbiology, Elected Fellow
American Association for the Advancement of Science, Elected Fellow
|Appointments||Damon Runyon-Walter Winchell Postdoctoral Fellow|
Our laboratory studies retroviruslike elements using the budding yeast (Saccharomyces cerevisiae) retrotransposon Ty3. Retrotransposons make up almost half of the human genome but their regulation and impact on genomic function is not yet well understood; we study Ty3 as a model for understanding both retrotransposons and also retroviruses. Ty3 studies have elucidated the roles of virus structural protein in capsid assembly, roles of nucleoporins in nuclear entry and roles of transcription factors in integration specificity. We are currently focused on understanding the role of non-coding RNA in expression of Ty3 and how RNA processing proteins help to localize and package the genomic RNA into particles. In addition, the laboratory is working to elucidate the genomic features which affect integration into chromosomal target sites. The laboratory uses a combination of molecular genetics, biochemistry and next generation sequencing to address these questions.
We also study metabolism of yeast as a model eukaryote. We developed a unique series of plasmids to allow combinatorial expression of genes for pathway engineering in Saccharomyces cerevisiae. However, S. cerevisiae is fermentative which restricts some of the metabolic studies that it supports. We therefore also study a yeast, Yarrowia lipolytica, which has aerobic metabolism more similar to that of humans than that of S. cerevisiae. Y lipolytica stores excess carbon as lipid rather than polysaccharide. We are performing computational modeling of S. cerevisiae and Y. lipolytica metabolism as well as using Y. lipolytica as a platform for biosustainable chemicals derived from acetyl-CoA precursors.
For more information, please see recent publications below or visit the laboratory homepage (http://http//sbspowerserver.biochem.uci.edu).
|Publications||Qi, X., Vargas, E., Larsen, L., Hung, S-P., Lathrop, R., Hatfield, G.W., and Sandmeyer, S.B. Directed DNA shuffling of retrovirus and retrotransposon integrase protein domains PLoS ONE (in press).|
|Clemens*, K., Beliakova-Bethell*, N., Bilanchone, V., Larsen, L. Z., Nguyen, K., and Sandmeyer, S. B. Different sequence requirements for Ty3 RNA association with P-body proteins and packaging. (2013) Virus Research 171, 319-331.|
|Qi X., and Sandmeyer S. (2013) Nonhomologous Recombination: Retrotransposons. In: Lennarz W.J. and Lane M.D. (eds.) The Encyclopedia of Biological Chemistry, vol. 3, pp. 283-291. Waltham, MA: Academic Press.|
|Liu, P., Chernyshov, A., Najdi, T. Fu, Y., Dickerson, J., Sandmeyer, S., Jarboe, L. (2013) Membrane Stress Caused by Octanoic acid in Saccharomyces cerevisiae Applied Microbiology and Biotechnology 97:3239-3252.|
|Qi, X. and Sandmeyer, S.B. In vitro targeting of strand transfer by the Ty3 retroelement integrase. (2012) J. Biol. Chem. 287, 18589-18595. PMCID 3365781|
|Qi*, X., Daily*, K., Nguyen*, K., Wang, H., Mayhew, D., Rigor, P., Forouzan,S., Johnston, M., Mitra, R.D., Baldi, P. and Sandmeyer, S.B. (2012) Retrotransposon profiling of RNA polymerase III initiation sites. Genome Res. 22, 681-92.|
Shen, M.W.Y., Fang, F., Sandmeyer, S., Da Silva, N.A.
Development and Characterization of a Vector Set with Regulated Promoters for Systematic Metabolic Engineering of Saccharomyces cerevisiae. (2012) Yeast 29, 495-503.
|Christiansen, K., Larsen, L.Z., Zhang, M., Kuznetsov, Y., Bilanchone, V., Beliakova-Bethell, N., Randall, A., DaSilva, R., Nagashima, K., McPherson, A., Baldi, P. and Sandmeyer, S.B. (2011) Ty3 spacer controls intracellular condensation and uncoating. Ty3 spacer controls intracellular condensation and uncoating. J. Virol. 2011 (Epub Jan26; PMID: 21270167; doi:10.1128/JVI.01055-10).|
|Zhang, M. *, Larsen, L.S.Z. * , Irwin, B., Bilanchone, V., and Sandmeyer, S.B. (2010) Ty3 Capsid subdomain interactions contribute to viruslike particle stability. Mobile DNA, 1:14.|
|Fang, F., Salmon, K., Shen, M., Aeling, K, Ito, E., Irwin, B., Tran, U., Hatfield, G.W., Da Silva, N.*, and Sandmeyer, S.* (2010) A combinatorial vector set for metabolic engineering in Saccharomyces cerevisiae. Yeast 28(2) 123-136 (Epub DOI: 10.1002/yea.1824).|
|Beliakova-Bethell, N., Terry, L.J., Bilanchone, V.W., DaSilva, R., Nagashima, K., Wente, S., and Sandmeyer, S.B. (2009) Ty3 nuclear entry is initiated by viruslike particle docking on nucleoporins. In press, J. Virol. 83: 11914-11925. Chosen for Nov Issue Spotlights.|
|Larsen, L.S.Z., Beliakova-Bethell, N., Bilanchone,V., Zhang, M., Lamsa, A., DaSilva, R., Hatfield, G.W., Nagashima, K., and Sandmeyer, S.B. (2008). Ty3 nucleocapsid controls localization of particle assembly. J. Virol. 82:2501-2514.|
|Larsen, L.S.Z., Kuznetsov, Y. McPherson , A. Hatfield, W. and Sandmeyer, S. (2007) Gag3 protein forms ordered particles in Escherichia coli. Virol. 370:223-227.|
|Larsen, L.S.Z., Zhang,M., Beliakova-Bethell, N., Bilanchone,V., Lamsa A., Nagashima, K., Najdi, R., Kosaka, K., Cheng, J., Baldi, P. Hatfield, G.W. and Sandmeyer, S.. (2007) Ty3 capsid mutations reveal early and late functions of the amino-terminal domain. J. Virol. 81:6957-6972.|
|Beliakova-Bethell, N., Beckham, C., Giddings, T.H. Jr., Winey, M., Parker, R., and Sandmeyer, S. (2006) Virus-like particles of the Ty3 retrotransposon assemble in association with P-body components. RNA 12:94-101.|
|Kuznetsov*, Y.G., Zhang*, M., Menees, T. McPherson, A, and Sandmeyer, S. (2005) Investigation by atomic force microscopy of the structure of Ty3 retrotransposon particles. J. Virol. 79: 8032-8045.|
|Irwin*, B., Aye*, M., Baldi, P., Beliakova-Bethell, N., Cheng, H., Dou, Y., Liou, W. and Sandmeyer, S.B. (2005) Retroviruses and yeast retrotransposons use overlapping sets of host genes. Gen. Res. 15:641-654.|
|Aye, M. Irwin, B., Archibald, H., and Sandmeyer, S.B. (2004) Host factors that affect Ty3 retrotransposition in Saccharomyces cerevisiae. Genetics 168, 1159-1176.|
*Yieh, L., *Hatzis, H., Kassavetis, G., Geiduschek, E.P. Sandmeyer, S.B. (2002) Mutational analysis of the TFIIIB-DNA target of Ty3 retroelement integration. J. Biol. Chem. 277:25920-25928.
Sandmeyer, S., Aye, M., and Menees, T. (2002) Ty3: A Position-Specific, Gypsylike Element in Saccharomyces cerevisiae. In Mobile DNA, ASM Press, Washington DC.
|Grants||Shared Instrumentation Grant (1S10RR025496-01, PI Sandmeyer) $500,000 High Throughput DNA Sequencer This grant was a cooperative effort of 20 investigators with the support of Schools of Biological Sciences, Medicine, and Information and Computer Sciences to purchase an Illumina GAIIX sequencing system.|
|#813570 09/01/08-08/31/13 NSF Host Institution University of Iowa (PI Shanks) Center for BioRenewable Chemicals, Subcontract to Sandmeyer total: This is an interdisciplinary project to use biosynthetic pathways in E. coli and S. cerevisiae to produce intermediates for industrial applications. The goal of the work in yeast in which the Sandmeyer laboratory is involved is to develop methods for production of short chain (<16 C) fatty acids in S. cerevisae.|
|R01 GM 33281-25 04/01/10-03/31/14 Ty3 Viruslike particle morphogenesis and host interactions. Retrotransposons compose large fractions of eukaryotic genomes. The class studied in the Sandmeyer laboratory is similar to retroviruses. It encodes structural proteins which make up a viruslike particle and reverse transcriptase which copies the RNA genome into cDNA. This retrotransposon is a good model system for retroviruses. The Sandmeyer laboratory is focused on understanding how the host supports assembly of particles and integration of the cDNA into genomic targets.|
Genetics Society of America
American Society for Microbiology
American Society for Biochemistry and Molecular Biology
American Association for the Advancement of Science
American Academy of Microbiology
Genomics High-Throughput Facility 1999—pres
Institute for Genomics and Bioinformatics 2009—pres
Cellular and Molecular Biosciences
|Research Centers||Institute for Genomics and Bioinformatics|
|Center for Virus Research|
|Chao Family Comprehensive Cancer Center|
|Center for Biorenewable Chemicals (ISU)|
|Link to this profile||http://www.faculty.uci.edu/profile.cfm?faculty_id=2247|