title: Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon.
abstract: BACKGROUND
  Transcript profiling of closely related species provides a means for identifying genes potentially important in species diversification. However, the predictive value of transcript profiling for inferring downstream-physiological processes has been unclear. In the present study we use shotgun proteomics to validate inferences from microarray studies regarding physiological differences in three Pachycladon species. We compare transcript and protein profiling and evaluate their predictive value for inferring glucosinolate chemotypes characteristic of these species.
  
  
  RESULTS
  Evidence from heterologous microarrays and shotgun proteomics revealed differential expression of genes involved in glucosinolate hydrolysis (myrosinase-associated proteins) and biosynthesis (methylthioalkylmalate isomerase and dehydrogenase), the interconversion of carbon dioxide and bicarbonate (carbonic anhydrases), water use efficiency (ascorbate peroxidase, 2 cys peroxiredoxin, 20 kDa chloroplastic chaperonin, mitochondrial succinyl CoA ligase) and others (glutathione-S-transferase, serine racemase, vegetative storage proteins, genes related to translation and photosynthesis). Differences in glucosinolate hydrolysis products were directly confirmed. Overall, prediction of protein abundances from transcript profiles was stronger than prediction of transcript abundance from protein profiles. Protein profiles also proved to be more accurate predictors of glucosinolate profiles than transcript profiles. The similarity of species profiles for both transcripts and proteins reflected previously inferred phylogenetic relationships while glucosinolate chemotypes did not.
  
  
  CONCLUSIONS
  We have used transcript and protein profiling to predict physiological processes that evolved differently during diversification of three Pachycladon species. This approach has also identified candidate genes potentially important in adaptation, which are now the focus of ongoing study. Our results indicate that protein profiling provides a valuable tool for validating transcript profiles in studies of adaptive divergence.
authors.affiliation: Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand.
authors.forename: Claudia
authors.initials: C
authors.lastname: Voelckel
authors.forename: Mehdi
authors.initials: M
authors.lastname: Mirzaei
authors.forename: Michael
authors.initials: M
authors.lastname: Reichelt
authors.forename: Zhiwei
authors.initials: Z
authors.lastname: Luo
authors.forename: Dana
authors.initials: D
authors.lastname: Pascovici
authors.forename: Peter B
authors.initials: PB
authors.lastname: Heenan
authors.forename: Silvia
authors.initials: S
authors.lastname: Schmidt
authors.forename: Bart
authors.initials: B
authors.lastname: Janssen
authors.forename: Paul A
authors.initials: PA
authors.lastname: Haynes
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Lockhart
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D019607:Brassicaceae / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D005961:Glucosinolates / Q000378:metabolism; D009520:New Zealand; D020411:Oligonucleotide Array Sequence Analysis; D040081:Protein Array Analysis; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D018749:RNA, Plant / Q000235:genetics
chemical_list: D005961:Glucosinolates; D020543:Proteome; D018749:RNA, Plant