Abstract
BackgroundTranscript 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.ResultsEvidence 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.ConclusionsWe 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.
Highlights
Transcript profiling of closely related species provides a means for identifying genes potentially important in species diversification
Our aim was to determine to what extent gene expression profiles were indicative of protein expression profiles and vice versa, and to evaluate both methods with respect to their potential for predicting physiological differences among New Zealand Pachycladon species
Transcriptome - proteome correlations To investigate the extent to which transcriptional patterns were congruent with protein expression patterns, we calculated correlation coefficients for 1074 genes surveyed by both transcript and protein profiling
Summary
Transcript profiling of closely related species provides a means for identifying genes potentially important in species diversification. DGE studies that compare expression profiles of closely related species, such as those that have formed during Late Tertiary radiation of New Zealand's alpine genera, might help to identify candidate genes that. Our aim was to determine to what extent gene expression profiles were indicative of protein expression profiles and vice versa, and to evaluate both methods with respect to their potential for predicting physiological differences among New Zealand Pachycladon species. For this purpose, we characterized glucosinolate chemotypes and evaluated the extent to which these were predicted from the protein and transcript expression data
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