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Title International reference centre for the genomics and diagnosis of viruses with small circular DNA
   
Acronym RCA Genomics
   
Duration 1 April 2007 - 1 April 2010
   
Project leader Holger Jeske, University of Stuttgart, Germany
   

Other project participants

Bruno Gronenborg, CNRS Plant Science Institute ISV, France
Susanne Ullmann*, Qiagen GmbH [Company], Germany
 Rafael E. Bejarano, University of Malaga, Spain
  
Funding National Institute for Agricultural Research (INRA), France 
   Research Centre Juelich – Project Management Juelich (FZJ-PTO) on behalf of the Federal Ministry of Education and Research (BMBF), Germany
  Ministry for Education and Science (MICINN), Spain  
   
  *participant with own funding
   
Total granted budget  € 1,031,039
   
Abstract  

A collaborative research project uniting participants of Universität Stuttgart, CNRS Gif, Universidad Malaga and Qiagen, Hilden is proposed to utilize the innovative power of rolling circle amplication (RCA) for diagnosis and genomics of viruses with small circular DNA, like geminiviruses and nanoviruses as well as satellite DNAs. Procedures and materials will be developed that allow the centralized analysis of infected plant samples from all over the world, with emphazisis on subtropical and tropical countries. A reference database will be established for plant protection measurements as open access. For functional genomics, RCA-based techniques will be developed to identify relevant genes in the interaction of viruses and hosts, with the primary goal to select or engineer virus resistance. The project is intended to provide added value to crop sustainablity of tomato, cotton, beet and cassava among others.
 
Progress
Hundreds of geminivirus-infected leaf samples have been collected from Brasil, Bolivia, Cuba, Germany, Iran as well as from the virus stock of the Institute of Biology in Stuttgart.
In addition, the Spanish partner performed the characterization of geminiviruses from hundreds of samples collected from different places, including the hosts tomato, cassava, sweet potato, grapevine, citrus from Perú, Venezuela, Uruguay, Argentina, Angola. Furthermore, RCA was used to study the effect of the presence of the Ty-1 gene of resistance to TYLCD on the diversifications of the population under mixed infection conditions in tomato plants, and to understand the effect of vector transmission and host adaptation in the structure of the populations of TYLCD-associated viruses variant causing the infection if any was detected. A high throughput cloning of the geminiviral DNAs has been established and sequencing has been considerably accelerated. The resultant protocols have be demonstrated during an RCA Summer School in Stuttgart (July 28th –August 8th, 2008) and will be shown during the next Summer School (August 3rd-14th, 2009) - which has been prepared for PhD students and advanced scientists involved in plant protection from all over the world. A new vector system for virus-induced gene silencing has been developed which has been proven to be a versatile tool in functional genomics. The French partner has succeeded for the first time to identify all necessary DNA components for plant-to-plant- as well as plant-to-insect-to-plant-transmission of a nanovirus using RCA and high-throughput sequencing.
  Figure 1 Geminivirus-infected leaf
 
Project website

http://www.uni-stuttgart.de/bio/bioinst/molbio/
 
Output from the project (publications, patents, data resources, etcetera)

Publications
Homs, M., Kober, S., Kepp, G., and Jeske, H. (2008). Mitochondrial plasmids of sugar beet amplified via rolling circle method detected during curtovirus screening. Virus Res. 136, 124-129.

Jeske, H. (2008). Geminiviruses. In "Torque Teno Virus, Current Topics in Microbiology and Immunology" (H. zur Hausen, de Villiers, E.-M., Ed.), pp. in press. Springer, Berlin.

Krenz, B., Wege, C., and Jeske, H. (2008). Abutilon mosaic virus as a stable and attenuated vector for virus-induced gene silencing and limited phloem-specific protein expression. Plant Mol. Biol. in revision.

Homs, M., Kober, S., Kepp, G., and Jeske, H. (2008). Mitochondrial plasmids of sugar beet amplified via rolling circle method detected during curtovirus screening. Virus Res. 136, 124-129.

Jeske, H. (2009). Geminiviruses. In "Torque Teno Virus: The Still Elusive Human Pathogens" (H. zur Hausen, de Villiers, E.-M., Ed.), Vol. 331, pp. 185-226. Springer, Berlin.

Kittelmann, K., Rau, P., Gronenborn, B., and Jeske, H. (2009). Plant geminivirus rep protein induces rereplication in fission yeast. J. Virol. 83, 6769-6778.

Paprotka, T., Boiteux, L. S., Fonseca, M. E. N., Resende, R. O., Jeske, H., Faria, J. C., and Ribeiro, S. G. (2009). Detection, diversity analysis and cloning of Brazilian sweet potato geminiviruses using rolling circle amplification. submitted.