Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon

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.

[1]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[2]  R. Crowhurst,et al.  Global gene expression analysis of apple fruit development from the floral bud to ripe fruit , 2008, BMC Plant Biology.

[3]  D. Kliebenstein,et al.  The Gene Controlling the Quantitative Trait Locus EPITHIOSPECIFIER MODIFIER1 Alters Glucosinolate Hydrolysis and Insect Resistance in Arabidopsis[W] , 2006, The Plant Cell Online.

[4]  D. Norton,et al.  Threatened and uncommon plants of New Zealand , 1999 .

[5]  J. Kelso,et al.  Comparison of Protein and mRNA Expression Evolution in Humans and Chimpanzees , 2007, PloS one.

[6]  D. Norton,et al.  Threatened and uncommon plants of New Zealand (2008 revision) , 2009 .

[7]  F. Bakker,et al.  Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae). , 2010, Molecular biology and evolution.

[8]  Jonathan I. Watkinson,et al.  Physiological and molecular adaptations to drought in Andean potato genotypes , 2008, Journal of experimental botany.

[9]  F. Pontén,et al.  Correlations between RNA and protein expression profiles in 23 human cell lines , 2009, BMC Genomics.

[10]  Rajeev K. Varshney,et al.  Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage , 2009, Journal of experimental botany.

[11]  P. Khaitovich,et al.  BMC Genomics BioMed Central Methodology article Estimating accuracy of RNA-Seq and microarrays with proteomics , 2022 .

[12]  L. Breci,et al.  Comprehensive proteomics in yeast using chromatographic fractionation, gas phase fractionation, protein gel electrophoresis, and isoelectric focusing , 2005, Proteomics.

[13]  A. Whitehead,et al.  Neutral and adaptive variation in gene expression. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[14]  R. Beavis,et al.  A method for reducing the time required to match protein sequences with tandem mass spectra. , 2003, Rapid communications in mass spectrometry : RCM.

[15]  Robertson Craig,et al.  TANDEM: matching proteins with tandem mass spectra. , 2004, Bioinformatics.

[16]  M. Washburn,et al.  Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors. , 2007, Molecular bioSystems.

[17]  Sixue Chen,et al.  A redox-active isopropylmalate dehydrogenase functions in the biosynthesis of glucosinolates and leucine in Arabidopsis. , 2009, The Plant journal : for cell and molecular biology.

[18]  E. Flemetakis,et al.  Co-localization of Carbonic Anhydrase and Phosphoenol-pyruvate Carboxylase and Localization of Pyruvate Kinase in Roots and Hypocotyls of Etiolated Glycine max Seedlings , 2009, International journal of molecular sciences.

[19]  Rachel E. Kerwin,et al.  A Novel 2-Oxoacid-Dependent Dioxygenase Involved in the Formation of the Goiterogenic 2-Hydroxybut-3-enyl Glucosinolate and Generalist Insect Resistance in Arabidopsis[C][W][OA] , 2008, Plant Physiology.

[20]  B. Huyghues-Despointes,et al.  Arabidopsis Vegetative Storage Protein Is an Anti-Insect Acid Phosphatase , 2005, Plant Physiology.

[21]  Gordon K. Smyth,et al.  Individual Channel Analysis of Two-Colour Microarrays , 2005 .

[22]  A. Hoffmann,et al.  Detecting genetic responses to environmental change , 2008, Nature Reviews Genetics.

[23]  P. Lockhart,et al.  Transcriptional and biochemical signatures of divergence in natural populations of two species of New Zealand alpine Pachycladon , 2008, Molecular ecology.

[24]  B. Genty,et al.  Characterization and expression analysis of genes encoding alpha and beta carbonic anhydrases in Arabidopsis. , 2007, Plant, cell & environment.

[25]  P. Heenan,et al.  Phylogeny, biogeography and adaptive radiation of Pachycladon (Brassicaceae) in the mountains of South Island, New Zealand , 2003 .

[26]  Andrew Emili,et al.  Integrating gene and protein expression data: pattern analysis and profile mining. , 2005, Methods.

[27]  A. Hoffmann,et al.  Towards genetic markers in animal populations as biomonitors for human-induced environmental change. , 2007, Ecology letters.

[28]  C. Plomion,et al.  Leaf proteome analysis of eight Populus ×euramericana genotypes: Genetic variation in drought response and in water‐use efficiency involves photosynthesis‐related proteins , 2009, Proteomics.

[29]  M. Reichelt,et al.  The Arabidopsis Epithiospecifier Protein Promotes the Hydrolysis of Glucosinolates to Nitriles and Influences Trichoplusia ni Herbivory Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010261. , 2001, The Plant Cell Online.

[30]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[31]  P. Lockhart,et al.  A Pleistocene inter-tribal allopolyploidization event precedes the species radiation of Pachycladon (Brassicaceae) in New Zealand. , 2009, Molecular phylogenetics and evolution.

[32]  H. Czosnek,et al.  Non-commercial Research and Educational Use including without Limitation Use in Instruction at Your Institution, Sending It to Specific Colleagues That You Know, and Providing a Copy to Your Institution's Administrator. All Other Uses, Reproduction and Distribution, including without Limitation Comm , 2022 .

[33]  M. Sugimoto,et al.  Localization and expression of serine racemase in Arabidopsis thaliana , 2009, Amino Acids.