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Yang X, Hu R, Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Cheol Yim W, Ha J, Heyduk K, Goodstein DM, Guo HB, Moseley RC, Fitzek E, Jawdy S, Zhang Z, Xie M, Hartwell J, Grimwood J, Abraham PE, Mewalal R, Beltrán JD, Boxall SF, Dever LV, Palla KJ, Albion R, Garcia T, Mayer JA, Don Lim S, Man Wai C, Peluso P, Van Buren R, De Paoli HC, Borland AM, Guo H, Chen JG, Muchero W, Yin Y, Jacobson DA, Tschaplinski TJ, Hettich RL, Ming R, Winter K, Leebens-Mack JH, Smith JAC, Cushman JC, Schmutz J, Tuskan GA. The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nat Commun 2017; 8:1899. [PMID: 29196618 PMCID: PMC5711932 DOI: 10.1038/s41467-017-01491-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 09/21/2017] [Indexed: 12/26/2022] Open
Abstract
Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generate a de novo genome assembly and genome-wide transcript expression data for Kalanchoë fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identify signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock, and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA.
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Deborah A Weighill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jungmin Ha
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Karolina Heyduk
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert C Moseley
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Elisabeth Fitzek
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Zhihao Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Meng Xie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James Hartwell
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Juan D Beltrán
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Susanna F Boxall
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Louisa V Dever
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Kaitlin J Palla
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Rebecca Albion
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Travis Garcia
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jesse A Mayer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Sung Don Lim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Paul Peluso
- Pacific Biosciences, Inc., 940 Hamilton Avenue, Menlo Park, CA, 94025, USA
| | - Robert Van Buren
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Henrique Cestari De Paoli
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Daniel A Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama
| | | | - J Andrew C Smith
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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Abraham PE, Yin H, Borland AM, Weighill D, Lim SD, De Paoli HC, Engle N, Jones PC, Agh R, Weston DJ, Wullschleger SD, Tschaplinski T, Jacobson D, Cushman JC, Hettich RL, Tuskan GA, Yang X. Transcript, protein and metabolite temporal dynamics in the CAM plant Agave. Nat Plants 2016; 2:16178. [PMID: 27869799 DOI: 10.1038/nplants.2016.178] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 10/20/2016] [Indexed: 05/19/2023]
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.
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Affiliation(s)
- Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Deborah Weighill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Sung Don Lim
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, Nevada 89557-0330, USA
| | | | - Nancy Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Piet C Jones
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Ryan Agh
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Timothy Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, Nevada 89557-0330, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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