Already a proven mechanism for drought resilience, crassulacean acid metabolism (CAM) is a specialized type of photosynthesis that maximizes water-use efficiency by means of an inverse (compared to C3 and C4 photosynthesis) day/night pattern of stomatal closure/opening to shift CO2 uptake to the night, when evapotranspiration rates are low. A systems-level understanding of temporal molecular and metabolic controls is needed to define the cellular behaviour underpinning CAM. Here, we report high-resolution temporal behaviours of transcript, protein and metabolite abundances across a CAM diel cycle and, where applicable, compare the observations to the well-established C3 model plant Arabidopsis. A mechanistic finding that emerged is that CAM operates with a diel redox poise that is shifted relative to that in Arabidopsis. Moreover, we identify widespread rescheduled expression of genes associated with signal transduction mechanisms that regulate stomatal opening/closing. Controlled production and degradation of transcripts and proteins represents a timing mechanism by which to regulate cellular function, yet knowledge of how this molecular timekeeping regulates CAM is unknown. Here, we provide new insights into complex post-transcriptional and -translational hierarchies that govern CAM in Agave. These data sets provide a resource to inform efforts to engineer more efficient CAM traits into economically valuable C3 crops.
This is a preview of subscription content, access via your institution
Open Access articles citing this article.
Biotechnology for Biofuels and Bioproducts Open Access 10 March 2023
Nature Communications Open Access 03 November 2021
Integration of proteome and transcriptome refines key molecular processes underlying oil production in Nannochloropsis oceanica
Biotechnology for Biofuels Open Access 18 June 2020
Subscribe to this journal
Receive 12 digital issues and online access to articles
$119.00 per year
only $9.92 per issue
Rent or buy this article
Prices vary by article type
Prices may be subject to local taxes which are calculated during checkout
Silvera, K. et al. Evolution along the crassulacean acid metabolism continuum. Funct. Plant Biol. 37, 995–1010 (2010).
Borland, A., Griffiths, H., Hartwell, J. & Smith, J. Exploiting the potential of plants with crassulacean acid metabolism for bioenergy production on marginal lands. J. Exp. Bot. 60, 2879–2896 (2009).
West-Eberhard, M. J., Smith, J. A. C. & Winter, K. Photosynthesis, reorganized. Science 332, 311–312 (2011).
Borland, A. M. et al. Engineering crassulacean acid metabolism to improve water-use efficiency. Trends Plant Sci. 30, 327–338 (2014).
Borland, A. M. & Yang, X. Informing the improvement and biodesign of crassulacean acid metabolism via system dynamics modelling. New Phytol. 200, 946–949 (2013).
DePaoli, H. C., Borland, A. M., Tuskan, G. A., Cushman, J. C. & Yang, X. Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities. J. Exp. Bot. 65, 3381–3393 (2014).
Winter, K., Garcia, M. & Holtum, J. On the nature of facultative and constitutive CAM: environmental and developmental control of CAM expression during early growth of Clusia, Kalanchoë, and Opuntia. J. Exp. Bot. 59, 1829–1840 (2008).
Winter, K. & Holtum, J. Facultative crassulacean acid metabolism (CAM) plants: powerful tools for unravelling the functional elements of CAM photosynthesis. J. Exp. Bot. 65, 3425–3441 (2014).
Chia, D. W., Yoder, T. J., Reiter, W. D. & Gibson, S. I. Fumaric acid: an overlooked form of fixed carbon in Arabidopsis and other plant species. Planta 211, 743–751 (2000).
Fahnenstich, H. et al. Alteration of organic acid metabolism in Arabidopsis overexpressing the maize C(4)NADP-malic enzyme causes accelerated senescence during extended darkness. Plant Physiol. 145, 640–652 (2007).
Osmond, C. B. et al. Regulation of malic-acid metabolism in crassulacean-acid-metabolism plants in the dark and light: in-vivo evidence from (13)C-labeling patterns after (13)CO 2 fixation. Planta 175, 184–192 (1988).
Arrizon, J., Morel, S., Gschaedler, A. & Monsan, P. Comparison of the water-soluble carbohydrate composition and fructan structures of Agave tequilana plants of different ages. Food Chem. 122, 123–130 (2010).
Mancilla-Margalli, N. & López, M. Water-soluble carbohydrates and fructan structure patterns from Agave and Dasylirion species. J. Agric. Food Chem. 54, 7832–7839 (2006).
Raveh, E., Wang, N. & Nobel, P. Gas exchange and metabolite fluctuations in green and yellow bands of variegated leaves of the monocotyledonous CAM species Agave americana. Physiol. Plant. 103, 99–106 (1998).
Wang, N. & Nobel, P. Phloem transport of fructans in the crassulacean acid metabolism species Agave deserti. Plant Physiol. 116, 709–714 (1998).
Horemans, N., Foyer, C., Potters, G. & Asard, H. Ascorbate function and associated transport systems in plants. Plant Physiol. Biochem. 38, 531–540 (2000).
Bartoli, C. G. et al. Inter-relationships between light and respiration in the control of ascorbic acid synthesis and accumulation in Arabidopsis thaliana leaves. J. Exp. Bot. 57, 1621–1631 (2006).
Dutilleul, C. et al. Leaf mitochondria modulate whole cell redox homeostasis, set antioxidant capacity, and determine stress resistance through altered signaling and diurnal regulation. Plant Cell 15, 1212–1226 (2003).
Foyer, C. H. & Noctor, G. Ascorbate and glutathione: the heart of the redox hub. Plant Physiol. 155, 2–18 (2011).
Lai, A. et al. CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses. Proc. Natl Acad. Sci. USA 109, 17129–17134 (2012).
Stangherlin, A. & Reddy, A. Regulation of circadian clocks by redox homeostasis. J. Biol. Chem. 288, 26505–26511 (2013).
Zhou, M. et al. Redox rhythm reinforces the circadian clock to gate immune response. Nature 523, 472–476 (2015).
Cheung, C. Y., Poolman, M. G., Fell, D. A., Ratcliffe, R. G. & Sweetlove, L. J. A diel flux balance model captures interactions between light and dark metabolism during day-night cycles in C3 and crassulacean acid metabolism leaves. Plant Physiol. 165, 917–929 (2014).
Lochner, A. et al. Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass. J. Proteome Res. 10, 5302–5314 (2011).
Saeed, A. et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34, 374–378 (2003).
Mockler, T. C. et al. The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. Cold Spring Harb. Symp. Quant. Biol. 72, 353–363 (2007).
Zhou, X. et al. CYCLIN h;1 regulates drought stress responses and blue light-induced stomatal opening by inhibiting reactive oxygen species accumulation in Arabidopsis. Plant Physiol. 162, 1030–1041 (2013).
Inada, S., Ohgishi, M., Mayama, T., Okada, K. & Sakai, T. RPT2 is a signal transducer involved in phototropic response and stomatal opening by association with phototropin 1 in Arabidopsis thaliana. Plant Cell 16, 887–896 (2004).
Tseng, T.-S. & Briggs, W. R. The Arabidopsis rcn1-1 mutation impairs dephosphorylation of Phot2, resulting in enhanced blue light responses. Plant Cell 22, 392–402 (2010).
Ceusters, J. et al. Light quality modulates metabolic synchronization over the diel phases of crassulacean acid metabolism. J. Exp. Bot. 65, 3705–3714 (2014).
Grams, T. & Thiel, S. High light-induced switch from C3-photosynthesis to crassulacean acid metabolism is mediated by UV-A/blue light. J. Exp. Bot. 53, 1475–1483 (2002).
Banerjee, R. & Batschauer, A. Plant blue-light receptors. Planta 220, 498–502 (2005).
Chater, C. et al. Elevated CO2-induced responses in stomata require ABA and ABA signaling. Curr. Biol. 25, 2709–2716 (2015).
Hashimoto, M. et al. Arabidopsis HT1 kinase controls stomatal movements in response to CO2 . Nat. Cell Biol. 8, 391–397 (2006).
Tian, W. et al. A molecular pathway for CO(2) response in Arabidopsis guard cells. Nat. Commun. 6, 6057 (2015).
Umezawa, T. et al. Type 2C protein phosphatases directly regulate abscisic acid-activated protein kinases in Arabidopsis. Proc. Natl Acad. Sci. USA 106, 17588–17593 (2009).
Xie, T. et al. Molecular mechanism for inhibition of a critical component in the Arabidopsis thaliana abscisic acid signal transduction pathways, SnRK2.6, by protein phosphatase ABI1. J. Biol. Chem. 287, 794–802 (2012).
Azoulay-Shemer, T. et al. Guard cell photosynthesis is critical for stomatal turgor production, yet does not directly mediate CO2-and ABA-induced stomatal closing. Plant J. 83, 567–581 (2015).
Wang, Y., Chen, Z., Zhang, B., Hills, A. & Blatt, M. PYR/PYL/RCAR abscisic acid receptors regulate K+ and Cl− channels through reactive oxygen species-mediated activation of Ca2+ channels at the plasma membrane of intact Arabidopsis guard cells. Plant Physiol. 163, 566–577 (2013).
Sze, H., Liang, F., Hwang, I., Curran, A. & Harper, J. Diversity and regulation of plant Ca2+ pumps: insights from expression in yeast. Annu. Rev. Plant Physiol. Plant Mol. Biol. 51, 433–462 (2000).
Jossier, M. et al. The Arabidopsis vacuolar anion transporter, AtCLCc, is involved in the regulation of stomatal movements and contributes to salt tolerance. Plant J. 64, 563–576 (2010).
Zybailov, B., Florens, L. & Washburn, M. Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors. Mol. Biosyst. 3, 354–360 (2007).
Howe, E., Sinha, R., Schlauch, D. & Quackenbush, J. RNA-Seq analysis in MeV. Bioinformatics 27, 3209–3210 (2011).
Walley, J. W. et al. Reconstruction of protein networks from an atlas of maize seed proteotypes. Proc. Natl Acad. Sci. USA 110, E4808–E4817 (2013).
Christopher, J. & Holtum, J. Patterns of carbohydrate partitioning in the leaves of crassulacean acid metabolism species during deacidification. Plant Physiol. 112, 393–399 (1996).
Yang, Q. et al. Overexpression of SOS (Salt Overly Sensitive) genes increases salt tolerance in transgenic Arabidopsis. Mol. Plant 2, 22–31 (2009).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18 (2012).
Huang, X. & Madan, A. CAP3: a DNA sequence assembly program. Genome Res. 9, 868–877 (1999).
Liu, C. et al. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics 13, 715 (2012).
This material is based on work supported by the Department of Energy Office of Science Genomic Science Program under award number DE-SC0008834. The authors would like to thank R. Giannone and M.A. Cushman for critical review and clarifying comments on the manuscript. This research used resources of the Compute and Data Environment for Science (CADES) and the Oak Ridge Leadership Computing Facility (OLCF) at the Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the US Department of Energy (under contract number DE-AC05-00OR22725).
The authors declare no competing financial interests.
About this article
Cite this article
Abraham, P., Yin, H., Borland, A. et al. Transcript, protein and metabolite temporal dynamics in the CAM plant Agave. Nature Plants 2, 16178 (2016). https://doi.org/10.1038/nplants.2016.178
This article is cited by
Biotechnology for Biofuels and Bioproducts (2023)
Allantoin improves salinity tolerance in Arabidopsis and rice through synergid activation of abscisic acid and brassinosteroid biosynthesis
Plant Molecular Biology (2023)
Proximate composition and spatio-temporal heterogeneity of phytochemicals in Agave sisalana Perrine (sisal) adapted in different agro-ecological zones of Punjab, Pakistan
Environmental Science and Pollution Research (2022)
Nature Communications (2021)
1H-NMR profile of mezcal and its distillation fractions using two sample preparation methods: direct analysis and solid-phase extraction
Chemical Papers (2021)