CONCLUSION
To date, detailed analyses of plant functions during a 24 h diurnal
cycle have mostly focused on genome-wide changes in gene expression.
Transcript-level changes can serve as a proxy for protein-level changes,
but in plants transcript levels often do not correlate with protein
abundance. While proteomes have a narrower dynamic range than
transcriptomes, they nevertheless complement transcriptome studies
because they provide direct insights into protein-level changes. Our
quantitative analysis of the proteome over a 12 h light : 12 h dark 24 h
photoperiod and the phosphoproteome at the L-D and D-L transitions
during the diurnal cycle in a single experimental workflow has generated
new information on diurnal abundance fluctuations and/or phosphorylation
changes for Arabidopsis proteins involved in different cellular and
biological processes (Figure 6). The identified proteins and
phosphoproteins provide a useful basis for further experimental studies.
In particular, it will be interesting to understand the specific
functions of diurnally fluctuating ribosomal proteins and other proteins
involved in translation considering that hundreds of ribosomal protein
isoforms are encoded by plant genomes with little information of what
dictates their combinatorial assembly. The regulation of protein
translation in plants at the protein complex level remains poorly
understood, but specific time-of-day abundance peaks for these proteins
suggests that temporal differences in the ribosome complex exists that
likely correlated with the specific time-of-day requirements of the
plant cell. Further elucidation of ribosome and protein translation
regulation will be instrumental in filling the current knowledge gap
between the transcriptome and proteome. Lastly, our phosphoproteome
analysis during the transitions from D-L and L-D provides new
information about candidate protein kinase sub-families catalyzing the
phosphorylation events, providing new opportunities for future
systems-level and targeted studies.