ABSTRACT
Future Challenges Christophe Plomion,1,a,* Delphine Vincent,1,b Frank Bedon,1,c Johann
Joets,2 Ludovic Bonhomme,3 Domenico Morabito,4 Sébastien Duplessis,5 Robert Nilsson,6,d Gunnar Wingsle,6,e Christer
Larsson,7 Yves Jolivet,8 Jenny Renaut,9 Olga Pechanova10 and Cetin Yuceer11
Integrated approaches that combine the systematic sequencing of expressed genes and the analysis of mRNA expression for a large number of genes are now considered strategies for tracking the genes of interest. However, while the poplar genome (Populus spp.; Tuskan et al. 2006) provides us with an overview of the genes in trees, it is becoming increasingly clear that this is only a very fragmentary beginning of understanding their role and function. The old paradigm of one gene for one protein is no longer valid, and in eukaryotic cells the situation is more like 6-8 proteins per gene. Thus, while there may be only 25,000 to 100,000 genes in a plant species, there
For affi liations see at the end of this chapter on page 165
are many more resultant proteins, including splice variants and essential post-transcriptional/translational modifi cations. Genome information is not suffi cient to defi ne all of these protein components. For example, studying mRNA quantities provides only a partial view of gene product expression due to: (i) large differences between mRNA and protein turnover (i.e., a protein can still be abundant while the mRNA is no longer detectable because its synthesis has stopped), (ii) post-translational modifi cations of proteins such as removal of signal peptides, phosphorylation and glycosylation, which play important roles in their activity and sub-cellular localization, and (iii) complex interactions with other proteins. These processes cannot be deduced from microarray or nucleic acid-based methodologies. The problem becomes even more complicated, because complex networks of proteins can be very divergent in different organs or developmental phases of the same organism, despite the same genomic information.
