Correlation of mRNA and protein abundance in the developing maize leaf

To help understand regulation of maize leaf blade development, including sink-source transitions and induction of C4 photosynthesis, we compared large scale quantitative proteome and transcriptomes collected at specific stages along the developmental maize leaf blade gradient. Proteome data were based on label-free shotgun proteomics (spectral counting) and transcript data were based on RNA-seq using the same source materials, and were previously published (Li et al. 2010, Majeran et al. 2010).Transcript and protein abundance followed near normal distributions, in contrast to several studies with other organisms. Protein observability correlated to transcript abundance following a =91lazy step function=92 similar as in bacteria and yeast. mRNA and protein abundance showed significant positive correlations (upto 0.8) for log-transformed length-weighted (NSAF and RPKM) and non-weighted abundances (NadjSPC and COV) in dependence of function and development. Correlations were much weaker in the leaf =91sink-source=92 transition zone=92, i.e. the zone with massive investments in leaf chloroplast biogenesis and build-up of photosynthetic capacity. Clustering analyses of gene-specific protein-mRNA ratios revealed coordinated shifts in control points in gene expression along the leaf blade developmental gradient. The highest protein/mRNA ratio for each gene generally corresponded to leaf developmental stages where the protein function was most important, with the exception of the 80S ribosome. Specific examples are discussed in the context of C4 photosynthesis, leaf development and sink-source transitions. This is the first large scale mRNA-protein correlation analysis in plants (maize) using label-free spectral counting for protein quantification and RNA-seq for mRNA abundance.