Why Proteomics?

Today, the use of genomic sequence data and transcriptomic methods allows molecular description of the evolution of whole plant genomes, as well as the regulation of homoelogous genes in polyploidy species. However, as the prime targets of evolutionary selection, phenotypes and biological mechanisms are essentially influenced by proteins rather than transcripts. Moreover, there is no linear correlation between RNA transcription and protein abundance existing, and no information on post-translational protein modification, which may play a key role in molecular interaction in cells, can be deduced from genomic study. Therefore, it is critical that we extend the frontier of functional genomics of evolutionary study into the realm of the proteome, which has emerged as a powerful approach for studying biological progresses and directly profiling changes in cells and tissues.

 Objectives:

Our research aims to develop our understanding how cotton proteomes respond to the evolutionary history, including natural polyploidization and human-mediated domestication. These in-depth functional genomic data are also expected to provide us new opportunities for cotton improvement.

1. To develop technology and tools for describing and studying the cotton fiber and seed proteome.

2. To describe the cotton proteome from the standpoint of fiber development, which will allow us to assess the changes that accompany the fiber evolution and domestication in the following study, and how this correlates with existing information on the transcriptome.

3. To understand how the proteome responds to genome doubling; that is, what is novel about polyploid cotton fiber and seed relative to that of its antecedent diploids?

4. To detail proteomic consequences of cotton fiber evolution and domestication; for example, to catalog the key proteins associated with and therefore possibly responsible for phenotype changes and important traits relevant to crop improvement.

 

Figure 1 The evolutionary history of diploid and allotetraploid cotton species. Images of a single seed with attached trichomes (“cotton fiber”) are shown from A-genome G. arboreum, D-genome G. raimondii, and a wild form (accession TX2094; YUC) and a domesticated stock TM1 (TM1) of G. hirsutum, a wild form (K101) and a modern cultivar (Pima S-7) of G. barbadense.

Laboratory methods

(1) protein extraction; see protocol

(2) separation or simplification of extracted proteins;

(3) quantitative analysis by two-dimensional electrophoresis (2-DE) based approach or mass spectrometry (MS) based approaches; see 2-DE protocol

(4) peptide analysis and protein identification by MS.

	Figure 2. 2-DE separation of seed proteins from G. hirsutum, Acala Maxxa. In the example shown, an IEF range of 4-7 was used.
	Figure 3. 2-DE separation of fiber proteins from G. barbadense, Pima S-7. In the example shown, an IEF range of 3-10 was used.