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.
Highlights
The Earth environment undergoes periodic changes, such as diurnal, lunar and solar cycles
We found that ca. 400 of genes from our report were defined as showing diurnal rhythmicality by Khan et al [19], which corresponds to ca. 30% of their set
Microarray data deliver information on plant functioning only at the transcriptome level, so their relevance to the true effector level of physiology must not be taken for granted. The value of such data is limited by the often sketchy description of genes represented by the microarray probes
Summary
The Earth environment undergoes periodic changes, such as diurnal, lunar and solar cycles. Living organisms have adapted to these changes and developed mechanisms to sense the cyclic signals from the environment allowing proper adjustment of their metabolism, growth and development These mechanisms involve endogenous oscillators and other clocks. In respect to photoperiodism, A. thaliana is a long-day plant, while maize, being of tropical origin, is a short-day plant This suggests that there could be substantial differences in the regulatory mechanisms underlying their diurnal rhythms. Numerous biochemical and physiological parameters of living organisms follow a circadian rhythm Such rhythmic behavior is 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. 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
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