Uncovering Transcriptional Gene Regulatory Networks Operating in the Facultative CAM Species, Mesembryanthemum crystallinum

Crassulacean acid metabolism (CAM) is a water-use efficient photosynthetic adaptation found in more than 6% of vascular plant species. This adaptation is distinguished by the temporal separation of primary C₄ and secondary C₃ carboxylation reactions to reduce daytime water loss. We investigated the underlying orchestration of transcriptional networks controlling the temporal separation of these competing carboxylation reactions on the facultative CAM ice plant, Mesembryanthemum crystallinum, performing C₃ and CAM (induced by water-deficit stress) over a 72 h time course using rhythmic and community-based ensemble gene regulatory network analyses. Rhythmic analyses revealed diel and circadian changes in transcript abundance patterns between the C₃ and CAM states that are involved in CAM adaptation and possibly their role in the regulation of CAM by the circadian clock. Ensemble transcriptional gene network and community analyses of the uniquely rhythmic 3,881 genes and 120 transcription factors upon CAM induction revealed a circadian clock-controlled community network. This community-based consensus network is comprised of 13 CAM-specific communities or gene groups. These gene groups were tested for Gene-Ontology-term enrichment. Our results tentatively identified CAM-specific transcriptional gene regulatory networks, and their putative transcription factors, which provide insights into the circadian clock-controlled transcriptional expression and regulation of CAM.