Proteome analysis of non-model plants: a challenging but powerful approach.
Biological research has focused in the past on model organisms and most of the functional genomics studies in the field of plant sciences are still performed on model species or species that are characterized to a great extent. However, numerous non-model plants are essential as food, feed, or energy resource. Some features and processes are unique to these plant species or families and cannot be approached via a model plant. The power of all proteomic and transcriptomic methods, that is, high-throughput identification of candidate gene products, tends to be lost in non-model species due to the lack of genomic information or due to the sequence divergence to a related model organism. Nevertheless, a proteomics approach has a great potential to study non-model species. This work reviews non-model plants from a proteomic angle and provides an outline of the problems encountered when initiating the proteome analysis of a non-model organism. The review tackles problems associated with (i) sample preparation, (ii) the analysis and interpretation of a complex data set, (iii) the protein identification via MS, and (iv) data management and integration. We will illustrate the power of 2DE for non-model plants in combination with multivariate data analysis and MS/MS identification and will evaluate possible alternatives.
Carpentier
Sebastien Christian
SC
Division of Crop Biotechnics, K.U.Leuven, Leuven, Belgium. sebastien.carpentier@biw.kuleuven.be
Panis
Bart
B
Vertommen
Annelies
A
Swennen
Rony
R
Sergeant
Kjell
K
Renaut
Jenny
J
Laukens
Kris
K
Witters
Erwin
E
Samyn
Bart
B
Devreese
Bart
B
D018506:Gene Expression Regulation, Plant; D010449:Peptide Mapping; D014674:Plant Proteins, Dietary / Q000032:analysis* / Q000737:chemistry; D010944:Plants / Q000235:genetics* / Q000378:metabolism*; D040901:Proteomics; D013048:Specimen Handling / Q000379:methods; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
D014674:Plant Proteins, Dietary