Rhythmic Diel Pattern of Gene Expression in Juvenile Maize Leaf

Abstract

BackgroundNumerous biochemical and physiological parameters of living organisms follow a circadian rhythm. Although such rhythmic behavior is particularly pronounced in plants, which are strictly dependent on the daily photoperiod, data on the molecular aspects of the diurnal cycle in plants is scarce and mostly concerns the model species Arabidopsis thaliana. Here we studied the leaf transcriptome in seedlings of maize, an important C4 crop only distantly related to A. thaliana, throughout a cycle of 10 h darkness and 14 h light to look for rhythmic patterns of gene expression.ResultsUsing DNA microarrays comprising ca. 43,000 maize-specific probes we found that ca. 12% of all genes showed clear-cut diel rhythms of expression. Cluster analysis identified 35 groups containing from four to ca. 1,000 genes, each comprising genes of similar expression patterns. Perhaps unexpectedly, the most pronounced and most common (concerning the highest number of genes) expression maxima were observed towards and during the dark phase. Using Gene Ontology classification several meaningful functional associations were found among genes showing similar diel expression patterns, including massive induction of expression of genes related to gene expression, translation, protein modification and folding at dusk and night. Additionally, we found a clear-cut tendency among genes belonging to individual clusters to share defined transcription factor-binding sequences.ConclusionsCo-expressed genes belonging to individual clusters are likely to be regulated by common mechanisms. The nocturnal phase of the diurnal cycle involves gross induction of fundamental biochemical processes and should be studied more thoroughly than was appreciated in most earlier physiological studies. Although some general mechanisms responsible for the diel regulation of gene expression might be shared among plants, details of the diurnal regulation of gene expression seem to differ between taxa.

Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm

“…The genes showing diurnal rhythm of transcription in control conditions have been discussed earlier (Jończyk et al 2011). Among the cold-responsive genes a statistical analysis distinguished genes whose diurnal profile of transcription was changed in the cold from genes whose transcription showed no temporal changes but was altered by cold.…”

“…In those cases, to fill-in the missing data and obtain a complete expression matrix we used the JBPCAfill program (Oba et al 2003) which estimates missing values by the PCA method. The completed data was normalized using loess method as described earlier (Jończyk et al 2011). Further analyses were run on expression fold-change values, i.e., relative to the time-zero sample, in JMP Genomics 6.0.3 (SAS Institute).…”

“…That the transcription of numerous genes is cyclic has been shown for several plant species, including A. thaliana (Harmer 2000), poplar and rice (Filichkin et al 2011), and maize (Hayes et al 2010;Khan et al 2010;Jończyk et al 2011). Kocsy et al (1997) showed that chilling (12 °C) changes the rhythmic expression of genes encoding enzymes involved in protection against oxidative stress in maize.…”

“…(Ibañez et al 2008) it is tempting to assume that the clock architecture and functioning are conserved in plants. Several clock components have also been found in maize (Hayes et al 2010;Khan et al 2010), however, due to its recent whole genome duplication, maize possibly bears two copies of each clock component, as exemplified by the GIGANTEA genes gigz1a and gigz1b (Miller et al 2008) as well as TOC1 homologs (Jończyk et al 2011). This makes it possible that the maize clock could exhibit certain idiosyncrasies, although some of the ortholog pairs (Hayes et al 2010;Khan et al 2010), but not all (Jończyk et al 2011), show congruent expression patterns.…”

“…Several clock components have also been found in maize (Hayes et al 2010;Khan et al 2010), however, due to its recent whole genome duplication, maize possibly bears two copies of each clock component, as exemplified by the GIGANTEA genes gigz1a and gigz1b (Miller et al 2008) as well as TOC1 homologs (Jończyk et al 2011). This makes it possible that the maize clock could exhibit certain idiosyncrasies, although some of the ortholog pairs (Hayes et al 2010;Khan et al 2010), but not all (Jończyk et al 2011), show congruent expression patterns. Indeed, not all plant clocks function exactly in the same manner as in the best-studied model A. thaliana, e.g., in the CAM plants Opuntia ficus-indica and Mesembryanthemum crystallinum (Boxall 2005;Mallona et al 2011).…”