ReviewCombining proteomic and genetic studies in plants
Introduction
With the completion of the sequence of the first plant genome, of Arabidopsis thaliana in 2000 [1], plant biology has also turn the century by entering the so-called post genomic era and, as other life sciences, has developed new approaches. We will briefly describe and discuss in the following pages the developments in plant proteomics and their relationships to plant genetics. Several reviews have been published in the last few years that can be read as a useful complement to the present contribution [2], [3], [4], [5]. As yet described in these reviews, the opportunity given to reveal several hundreds to few thousands of gene products on one single 2D gel—by the means of two-dimensional electrophoresis of denatured proteins—permitted to examine:
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variations in gene expression, according to the plant development and in response to various abiotic and biotic stresses or treatments, leading to the identification of regulated proteins;
- (2)
genetic variations: mutants lines have been characterized, genetic distances have been estimated, phylogenetic relationships have been established and factors controlling protein expression have been mapped.
The position of proteins on 2D gels depends on their primary sequence, and any mutation (amino acid substitution, insertion/deletion) that has an effect on the pI or on the mobility in SDS–PAGE will modify the position of the protein: they lead to position shift (PS) variants (Fig. 1). Mutations leading to the absence of the protein will produce presence/absence (P/A) variations (Fig. 1). The latter can also be due to PS: one of the two spots being masked by another spot or its pI being outside of the pH range of the isoelectrofocusing. In most cases, observed PS and P/A have been shown to be under monogenic control and indeed correspond to allelic variations (reviewed in Ref. [6]). Such markers are physiologically relevant in that they reveal loci whose transcripts are translated in the organ analysed. The other type of variations that can be observed in 2DE is the variation in amount of a same protein spot in different genotypes (genetically determined quantitative variations) or in different developmental stages or organs.
Although the term “proteome” was introduced in a conference by Wilkins in 1994, to refer to the total protein complement of a genome, the roots of this modern concept date back to 1975 with high-resolution two-dimensional polyacrylamide gel electrophoresis. 2DE is still today the most resolutive technique for the analysis of complex protein mixtures, but it does not permit protein identification. The development of mass spectrometry techniques (peptide mass fingerprinting and peptide sequencing (reviewed in Ref. [7])), not only allowed to identify the proteins showing variations in function because of genetic variation or physiological changes, but also made it possible to undertake protein inventories in different plant structures (organs, tissues, cells, organelles, ribosomes). The topics discussed in this review, on genetically oriented plant proteomics, are summarized in Fig. 2.
Section snippets
Differentiation and development
The proteomes of the different organs of a plant are obviously different. They are often studied separately, e.g., in proteome databases [8], but comparisons between them are scarce, and most of them are actually related to the study of genetic variations.
Several studies have demonstrated that organ-specific proteins are more variable between genotypes than organ-unspecific proteins, and that the level of genetic variability depends on the organ or tissue considered. In maritime pine, Bahrman
Abiotic stresses
A great interest has been brought to plant response to abiotic stresses, mainly because of possible applications to breeding programs of cultivated species.
Elevated temperatures induce, in plants as in other organisms, the synthesis of heat shock proteins (HSPs). Their synthesis is correlated to the acquisition of thermal tolerance, i.e., the ability to withstand higher temperatures. Plants differ from other organisms in that they synthesize a great number of low-molecular mass HSPs (LMW-HSPs),
Polymorphism of genes encoding the proteins
As far as their products show an allelic variation, the genes encoding the revealed proteins can be mapped on the chromosomes, allowing expressed genes to be added to the genetic maps mainly established with non-coding DNA-markers. Qualitative variants such as P/A and PS (Fig. 1) have also been widely used to study relationships between genotypes, populations, species and genus.
Protein quantity loci
Damerval et al. [98] were the first in 1994 who investigate the genetic determinism of quantitative variation of proteins separated by 2DE using a QTL (quantitative trait loci) detection strategy. They used a linkage map constructed with RFLPs and PS loci segregating in a F2 progeny of maize to locate by interval mapping [99], the “PQLs” (protein quantity loci), that explain part of the spot intensity variation. For the 72 proteins analyzed, 70 PQLs were detected for 42 proteins, 20 of them
Conclusion
Even if proteomic studies in plants have been undertaken for 20 years, plant proteomics is still in its infancy. It is only during the last few years that the application of mass spectrometry, together with the availability of one fully sequenced plant genome and, in many agronomic species, of thousands of sequenced cDNAs (ESTs), have permitted to go further than using the 2DE as a source of genetic markers.
Every experiment published in plant proteomics today is accompanied by a list of the
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