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Proteomic analysis of cellular compartments provides essential insight into the subcellular location of a specific protein or protein complex; a valuable step towards understanding protein function and something that cannot be accurately predicted from primary sequence. Localization information also helps in the identification of protein interactions and provides a means to assess targeting, trafficking and residence in multiple compartments. Moreover, the analysis of a subcellular proteome has the advantage of requiring "biological pre-fractionation," substantially enhancing the detection of lower abundance proteins.
The purpose of this NSF-funded project is to catalog and study the dynamic properties of the cell wall proteome, or secretome, using
tomato (Solanum lycopersicum) as a model system.
This will be achieved by coupling isotopic peptide labeling and shotgun mass spectrometry-based sequencing of highly enriched cell wall protein extracts with a range of newly developed functional screens and bioinformatics tools. These approaches will then be applied to characterize quantitative and qualitative changes in the wall proteome during fruit ripening and induction of defense responses. Additionally, a coordinated study will be performed of the tomato fruit secretome using protein expression profiling and microarray-based transcriptomics in wild type and ripening mutant fruit. This study in tomato will lay the foundation for a long-term exploration of the diversity of cell wall proteomes in a range of plant species.
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- Identify extracellular proteins:
- Extraction and anlysis of enriched cell wall protein extracts. Techniques have been developed to isolate extracellular proteins from various plant tissues, whilst minimizing contamination with intracellular proteins. Post-translational modification (e.g. glycosylation and phosphorylation) of proteins in these extracts will also be studied.
- Computational prediction of secreted proteins. Bioinformatics tools are under development to allow a more accurate in silico prediction of the secretome.
- Functional screens for secreted proteins. We have adopted a number of high throughput functional approaches to identify secreted proteins from a range of eukaryotes, including an enhanced yeast secretion trap (YST) screen and the NIP assay.
- Comparative analysis of the cell wall proteome in ripening tomato fruit and in tomato leaves following defense response elicitation.
- Integrated cell wall proteome and transcriptome expression profiling. Dynamic changes in the wall proteome will be compared with changes in the cognate transcriptome using micro-array analysis.
- Education, Training, and Outreach. A number of education and training opportunities in plant proteomics and cell wall biology have been established. Internships are available
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Upcoming Meetings
Solanaceae 2008 Cologne, Germany, Oct 12-16
2008 Plant Polysaccharide Workshop Aug 3-5, Sigtuna, Sweden
ASPB 2008 June 26-July 1, Merida, Mexico
ASMS meeting June 1-5, Denver, CO
Past Meetings
Cell Wall 2007 - Copenhagen
Solanaceae 2007 - Jeju Island
Genome to Proteome #7 - Siena
Jobs
The Rose lab is currently seeking a postdoctoral research associate with
an interest in plant proteomics, or fruit development and ripening.
Experience in mass spectrometry and plant molecular biology would
be an advantage, and good communication skills are critical.
Please contact Joss Rose if interested:
jr286@cornell.edu
Workshop
The annual summer proteomics workshop will be held in July 2008.
Please contact Joss Rose if interested :
jr286@cornell.edu
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External Links |
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Funding Summary
This project and database are funded by National Science Foundation Grant
0606595.
For questions and comments regarding the SecreTom project, please contact Jocelyn Rose at jr286@cornell.edu
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