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Transcript, protein and metabolite temporal dynamics in the CAM plant Agave

Nature Plants volume 2, Article number: 16178 (2016) Cite this article

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Abstract

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.

The water-use efficiency of Agave spp. hinges on crassulacean acid metabolism (CAM), a specialized mode of photosynthesis that evolved from ancestral C3 photosynthesis in response to water and CO2 limitation1 and is found in ∼6.5% of higher plants. Whereas C3 photosynthesis produces a three-carbon (3-C) molecule for carbon fixation during the day, CAM generates a four-carbon organic acid from carbon fixation at night. In CAM, this nocturnal carboxylation reaction is catalysed by phosphoenolpyruvate carboxylase (PEPC), and the 3-C substrate phosphoenolpyruvate (PEP) is supplied by the glycolytic breakdown of carbohydrate formed during the previous day. The nocturnally accumulated malic acid is stored overnight in a central vacuole, and during the subsequent day malate is decarboxylated to release CO2 at an elevated concentration for Rubisco in the chloroplast. The diel separation of carboxylases in CAM is accompanied by an inverse (compared with C3 and C4 photosynthesis-performing species) day/night pattern of stomatal closure/opening that results in improved water-use efficiency (CO2 fixed per unit water lost) that is up to sixfold higher than that of C3 photosynthesis plants and up to threefold higher than that of C4 photosynthesis plants under comparable conditions2.

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Figure 1: CAM exhibits rescheduled central metabolism and redox homeostasis relative to C3.
Figure 2: Temporal changes in Agave gene expression across the diel cycle.
Figure 3: Diel gene expression and the rescheduling of stomatal movement-related genes in Agave compared with Arabidopsis.
Figure 4: Temporal changes in protein abundances in Agave across the diel cycle.

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Acknowledgements

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).

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Authors and Affiliations

  1. Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, Tennessee, USA

    Paul E. Abraham & Robert L. Hettich

  2. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, Tennessee, USA

    Hengfu Yin, Anne M. Borland, Deborah Weighill, Henrique Cestari De Paoli, Nancy Engle, Piet C. Jones, Ryan Agh, David J. Weston, Timothy Tschaplinski, Daniel Jacobson, Gerald A. Tuskan & Xiaohan Yang

  3. School of Biology, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK

    Anne M. Borland

  4. The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, 37996, Tennessee, USA

    Deborah Weighill, Piet C. Jones & Daniel Jacobson

  5. Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, 89557-0330, Nevada, USA

    Sung Don Lim & John C. Cushman

  6. Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, Tennessee, USA

    Stan D. Wullschleger

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Contributions

X.Y., G.A.T., P.E.A. and R.L.H. contributed to conception and design of the experiment; P.A., H.Y., A.M.B., S.D.L., H.C.D.P., N.E., R.A. and T.T. contributed to the acquisition of data; and P.A., H.Y., A.B., D.J.W., P.C.J., D.J., T.T. and J.C.C. contributed to data analysis and interpretation; P.A., X.Y., G.T. and A.B. drafted the manuscript and all authors critically revised and approved the final version of the manuscript for publication.

Corresponding author

Correspondence to Xiaohan Yang.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figures 1–8, Supplementary Table Legends 1–17, Supplementary Notes, Supplementary References. (PDF 1380 kb)

Supplementary Tables 1–17

Supplementary Tables 1–17. (XLSX 46444 kb)

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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

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