Submitted to: Plant Journal
Publication Type: Peer reviewed journal
Publication Acceptance Date: 6/27/2004
Publication Date: 9/7/2004
Citation: Rose, J.K., Bashir, S., Giovannoni, J.J., Jahn, M.M., Saravanan, R.S. 2004. Tackling the plant proteome: practical approaches, hurdles and experimental tools. Plant Journal. 39:715-733. Interpretive Summary: The study of complex biological questions through comparative proteomics is becoming increasingly attractive to plant biologists as the rapidly expanding plant genomic and EST sequence databases provide improved opportunities for protein identification. This report focuses on practical issues associated with comparative proteomic analysis including the challenges of effective protein extraction and separation from plant tissues, the pros and cons of 2-D gel-based analysis and the problems of identifying proteins from species that are not necessarily considered to be models for functional genomics. Specific points relative to potential and limitations are illustrated using data from an ongoing study of the tomato and pepper fruit proteomes.
Technical Abstract: While quantitative analysis of a major portion of a plant proteome is not yet within reach, it is currently possible, at a reasonable cost, to undertake a comparative protein profiling analysis and to assess expression of significant numbers of polypeptides. This narrow window on the proteome may not provide the more comprehensive survey that is afforded by microarray analysis, but the advantages of surveying protein expression still more than justify this approach. In this sense, transcript and protein profiling are currently complementary, rather than equivalent fields and are typically used to answer different biological questions. This disparity will decrease as future technologies increase the breath of the proteome that can be studied, but it is likely to be some considerable time before plant transcriptomes and proteome analyses can be fully and seamlessly integrated. While much progress has been made in plant proteomics, it is important to consider the theoretical and practical limitations and to have an appreciation of what can and cannot currently be achieved when evaluating plant protein expression, particularly when considering cost and availability of the specialist instrumentation that is typically required. This report outlines some of the existing challenges and rate limiting steps, which span protein extraction, separation and the critical importance of an extensive affiliated DNA sequence data set and bioinformatics support.