Research Accomplishment Reports 2010

Advanced Genetic Technologies, KY

C.L. Schardl
Department of Plant Pathology

 

Non-Technical Summary

The genome of an organism represents the total of all genes, which are encoded in the base sequences of DNA of that organism. In order for a gene to be expressed, it must first be transcribed into RNA molecules, each similar in sequence to a DNA segment. Then, the RNAs are spliced and processed into mRNAs, which are then translated to give functional proteins. The entire set of mRNAs in a cell, tissue or organism is called its transcriptome. Analysis of whole-transcriptome sequence is key to understanding how genomes direct the organism's form, development, behavior, and responses to the environment. New technologies such as pyrosequencing have greatly increased DNA sequencing rates and reduced costs. In this study, several strategies will be tested for pyrosequencing of transcriptomes. Once these protocols are refined, they will be applied to various organisms of relevance to agricultural research, including plants, insects, and various pathogens and parasites. The results will serve as preliminary data for competitively funded research programs.

2010 Project Description

The Advanced Genetic Technologies Center at the University of Kentucky College of Agriculture sequenced the genomes of Peronospora tabacina, an oomycete pathogen of plants, and viruses that enable wasps to parasitize caterpillars (Lepidoptera larvae). In addition, draft genome sequences were produced for two grass symbionts, namely Epichloe festucae and Neotyphodium coenophialum, which produce mycotoxins that can cause toxicosis in livestock, Transcriptome sequencing was conducted for Sinningia speciosa, a plant model for tuber formation. Bioinformatic analysis was conducted on the transcriptome and genome sequences. Results contributed to 37 published research papers.

2010 Impact

The molecular sequences determined and annotated in this project contributed new knowledge on the biology of plants, plant pathogens and symbionts, and biological agents for potential control of insects.

2010 Publications

Korenkov V, King B, Hirschi K, Wagner GJ (2009) Root-selective expression of AtCAX4 and AtCAX2 results in reduced lamina cadmium in field-grown Nicotiana tabacum L. Plant Biotechnology Journal 7: 219-226

Li ZH, Pogany J, Panavas T, Xu K, Esposito AM, Kinzy TG, Nagy PD (2009) Translation elongation factor 1A is a component of the Tombusvirus replicase complex and affects the stability of the p33 replication co-factor. Virology 385: 245-260

Li ZH, Pogany J, Tupman S, Esposito AM, Kinzy TG, Nagy PD (2010) Translation elongation factor 1A facilitates the assembly of the Tombusvirus replicase and stimulates minus-strand synthesis. PLoS Pathogens 6: e1001175

Maiti I, Chatterjee A, Das N, Raha S, Babbitt R, Huang QW, Zaitlin D, Fan ZM, Kurt W, Charles L, Kong Q (2010) Expression of engineered xylan-degrading chimeric enzymes for bioenergy and biofuel applications. In Vitro Cellular & Developmental Biology-Animal 46: S45-S45

Mendu V, Chiu MH, Barajas D, Li ZH, Nagy PD (2010) Cpr1 cyclophilin and Ess1 parvulin prolyl isomerases interact with the Tombusvirus replication protein and inhibit viral replication in yeast model host. Virology 406: 342-351

Nagy PD, Pogany J (2010) Global genomics and proteomics approaches to identify host factors as targets to induce resistance against tomato bushy stunt virus. In Natural and Engineered Resistance to Plant Viruses, Part II, Vol 76, pp 123-177

Pathak KB, Nagy PD (2009) Defective Interfering RNAs: Foes of Viruses and Friends of Virologists. Viruses-Basel 1: 895-919

Pattanaik S, Kong Q, Zaitlin D, Werkman JR, Xie CH, Patra B, Yuan L (2010) Isolation and functional characterization of a floral tissue-specific R2R3 MYB regulator from tobacco. Planta 231: 1061-1076

Sasvari Z, Bach S, Blondel M, Nagy PD (2009) Inhibition of RNA recruitment and replication of an RNA virus by acridine derivatives with known anti-prion activities. PLoS One 4: e7376

Sasvari Z, Nagy PD (2010) Making of viral replication organelles by remodeling interior membranes. Viruses-Basel 2: 2436-2442

Schardl CL (2010) The epichloae, symbionts of the grass subfamily Pooideae. Annals of the Missouri Botanical Garden 97: 646-665

Seebold KW, De Sa P, Vincelli P (2009) First report of tomato yellow leaf curl virus in Kentucky. Phytopathology 99: S200-S200

Sharma M, Sasvari Z, Nagy PD (2010) Inhibition of sterol biosynthesis reduces Tombusvirus replication in yeast and plants. Journal of Virology 84: 2270-2281

 

Tang GL (2010) Gene regulation by small RNAs and the technological application in plants. In Vitro Cellular & Developmental Biology-Animal 46: S212-S213

Tang GL (2010) Plant microRNAs: An insight into their gene structures and evolution. Seminars in Cell & Developmental Biology 21: 782-789

Wang RYL, Stork J, Nagy PD (2009) A key role for heat shock protein 70 in the localization and insertion of Tombusvirus replication proteins to intracellular membranes. Journal of Virology 83: 3276-3287

Wang RYL, Stork J, Pogany J, Nagy PD (2009) A temperature sensitive mutant of heat shock protein 70 reveals an essential role during the early steps of Tombusvirus replication. Virology 394: 28-38

Wang WX, Wilfred BR, Madathil SK, Tang GL, Hu YL, Dimayuga J, Stromberg AJ, Huang QW, Saatman KE, Nelson PT (2010) miR-107 regulates granulin/progranulin with implications for traumatic brain injury and neurodegenerative disease. American Journal of Pathology 177: 334-345

Webb B, Fisher T, Nusawardani T (2009) The natural genetic engineering of Polydnaviruses. In G Witzany, ed, Natural Genetic Engineering and Natural Genome Editing, Vol 1178, pp 146-156

Wu BD, Pogany J, Na H, Nicholson BL, Nagy PD, White KA (2009) A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes. PLoS Pathogens 5

Zaitlin D, Pierce AJ (2010) Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S-speciosa. Genome 53: 1066-1082

Zhang DX, Stromberg AJ, Spiering MJ, Schardl CL (2009) Coregulated expression of loline alkaloid-biosynthesis genes in Neotyphodium uncinatum cultures. Fungal Genetics and Biology 46: 517-530

Barajas D, Jiang Y, Nagy PD (2009) A unique role for the host ESCRT proteins in replication of Tomato bushy stunt virus. PLoS Pathogens 5: e1000705

Barajas D, Li ZH, Nagy PD (2009) The Nedd4-type Rsp5p ubiquitin ligase inhibits Tombusvirus replication by regulating degradation of the p92 replication protein and decreasing the activity of the tombusvirus replicase. Journal of Virology 83: 11751-11764

Barajas D, Nagy PD (2010) Ubiquitination of Tombusvirus p33 replication protein plays a role in virus replication and binding to the host Vps23p ESCRT protein. Virology 397: 358-368

Book AJ, Smalle J, Lee KH, Yang PZ, Walker JM, Casper S, Holmes JH, Russo LA, Buzzinotti ZW, Jenik PD, Vierstra RD (2009) The RPN5 subunit of the 26S proteasome is essential for gametogenesis, sporophyte development, and c-complex assembly in Arabidopsis. Plant Cell 21: 460-478

Chatterjee A, Das NC, Raha S, Babbit R, Huang QW, Zaitlin D, Maiti IB (2010) Production of xylanase in transgenic tobacco for industrial use in bioenergy and biofuel applications. In Vitro Cellular & Developmental Biology-Plant 46: 198-209

Eaton CJ, Cox MP, Ambrose B, Becker M, Hesse U, Schardl CL, Scott B (2010) Disruption of signaling in a fungal-grass symbiosis leads to pathogenesis. Plant Physiology 153: 1780-1794

Florea S, Andreeva K, Machado C, Mirabito PM, Schardl CL (2009) Elimination of marker genes from transformed filamentous fungi by unselected transient transfection with a Cre-expressing plasmid. Fungal Genetics and Biology 46: 721-730

Gu M, Xu K, Chen AQ, Zhu YY, Tang GL, Xu GH (2010) Expression analysis suggests potential roles of microRNAs for phosphate and arbuscular mycorrhizal signaling in Solanum lycopersicum. Physiologia Plantarum 138: 226-237

Guedira M, Brown-Guedira G, Van Sanford D, Sneller C, Souza E, Marshall D (2010) Distribution of Rht genes in modern and historic winter wheat cultivars from the eastern and central USA. Crop Science 50: 1811-1822

Jaag HM, Nagy PD (2009) Silencing of Nicotiana benthamiana Xrn4p exoribonuclease promotes Tombusvirus RNA accumulation and recombination. Virology 386: 344-352

Jaag HM, Nagy PD (2010) The combined effect of environmental and host factors on the emergence of viral RNA recombinants. PLoS Pathogens 6: e1001156

Jaag HM, Pogany J, Nagy PD (2010) A host Ca2+/Mn2+ ion pump is a factor in the emergence of viral RNA recombinants. Cell Host & Microbe 7: 74-81

Jia XY, Ren LG, Chen QJ, Li RZ, Tang GL (2009) UV-B-responsive microRNAs in Populus tremula. Journal of Plant Physiology 166: 2046-2057

Jiang Y, Cheng CP, Serviene E, Shapka N, Nagy PD (2010) Repair of lost 5 ' terminal sequences in Tombusviruses: Rapid recovery of promoter- and enhancer-like sequences in recombinant RNAs. Virology 404: 96-105

Jiang Y, Li ZH, Nagy PD (2010) Nucleolin/Nsr1p binds to the 3 ' noncoding region of the Tombusvirus RNA and inhibits replication. Virology 396: 10-20