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Guan Q, Kong W, Tan B, Zhu W, Akter T, Li J, Tian J, Chen S. Multiomics unravels potential molecular switches in the C 3 to CAM transition of Mesembryanthemum crystallinum. J Proteomics 2024; 299:105145. [PMID: 38431086 DOI: 10.1016/j.jprot.2024.105145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Mesembryanthemum crystallinum (common ice plant), a facultative CAM plant, shifts from C3 to CAM photosynthesis under salt stress, enhancing water use efficiency. Here we used transcriptomics, proteomics, and targeted metabolomics to profile molecular changes during the diel cycle of C3 to CAM transition. The results confirmed expected changes associated with CAM photosynthesis, starch biosynthesis and degradation, and glycolysis/gluconeogenesis. Importantly, they yielded new discoveries: 1) Transcripts displayed greater circadian regulation than proteins. 2) Oxidative phosphorylation and inositol methylation may play important roles in initiating the transition. 3) V-type H+-ATPases showed consistent transcriptional regulation, aiding in vacuolar malate uptake. 4) A protein phosphatase 2C, a major component in the ABA signaling pathway, may trigger the C3 to CAM transition. Our work highlights the potential molecular switches in the C3 to CAM transition, including the potential role of ABA signaling. SIGNIFICANCE: The common ice plant is a model facultative CAM plant, and under stress conditions it can shift from C3 to CAM photosynthesis within a three-day period. However, knowledge about the molecular changes during the transition and the molecular switches enabling the transition is lacking. Multi-omic analyses not only revealed the molecular changes during the transition, but also highlighted the importance of ABA signaling, inositol methylation, V-type H+-ATPase in initiating the shift. The findings may explain physiological changes and nocturnal stomatal opening, and inform future synthetic biology effort in improving crop water use efficiency and stress resilience.
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Affiliation(s)
- Qijie Guan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Wenwen Kong
- College of Life Sciences, Northeast Agricultural University, Harbin 150040, China
| | - Bowen Tan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Wei Zhu
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou 310002, China
| | - Tahmina Akter
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Jing Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150040, China
| | - Jingkui Tian
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou 310002, China
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA.
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2
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Gilman IS, Smith JAC, Holtum JAM, Sage RF, Silvera K, Winter K, Edwards EJ. The CAM lineages of planet Earth. ANNALS OF BOTANY 2023; 132:627-654. [PMID: 37698538 PMCID: PMC10799995 DOI: 10.1093/aob/mcad135] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/09/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND AND SCOPE The growth of experimental studies of crassulacean acid metabolism (CAM) in diverse plant clades, coupled with recent advances in molecular systematics, presents an opportunity to re-assess the phylogenetic distribution and diversity of species capable of CAM. It has been more than two decades since the last comprehensive lists of CAM taxa were published, and an updated survey of the occurrence and distribution of CAM taxa is needed to facilitate and guide future CAM research. We aimed to survey the phylogenetic distribution of these taxa, their diverse morphology, physiology and ecology, and the likely number of evolutionary origins of CAM based on currently known lineages. RESULTS AND CONCLUSIONS We found direct evidence (in the form of experimental or field observations of gas exchange, day-night fluctuations in organic acids, carbon isotope ratios and enzymatic activity) for CAM in 370 genera of vascular plants, representing 38 families. Further assumptions about the frequency of CAM species in CAM clades and the distribution of CAM in the Cactaceae and Crassulaceae bring the currently estimated number of CAM-capable species to nearly 7 % of all vascular plants. The phylogenetic distribution of these taxa suggests a minimum of 66 independent origins of CAM in vascular plants, possibly with dozens more. To achieve further insight into CAM origins, there is a need for more extensive and systematic surveys of previously unstudied lineages, particularly in living material to identify low-level CAM activity, and for denser sampling to increase phylogenetic resolution in CAM-evolving clades. This should allow further progress in understanding the functional significance of this pathway by integration with studies on the evolution and genomics of CAM in its many forms.
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Affiliation(s)
- Ian S Gilman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - Joseph A M Holtum
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Katia Silvera
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Department of Botany & Plant Sciences, University of California, Riverside, CA, USA
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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3
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Leverett A, Borland AM. Elevated nocturnal respiratory rates in the mitochondria of CAM plants: current knowledge and unanswered questions. ANNALS OF BOTANY 2023; 132:855-867. [PMID: 37638861 PMCID: PMC10799998 DOI: 10.1093/aob/mcad119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/14/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023]
Abstract
Crassulacean acid metabolism (CAM) is a metabolic adaptation that has evolved convergently in 38 plant families to aid survival in water-limited niches. Whilst primarily considered a photosynthetic adaptation, CAM also has substantial consequences for nocturnal respiratory metabolism. Here, we outline the history, current state and future of nocturnal respiration research in CAM plants, with a particular focus on the energetics of nocturnal respiratory oxygen consumption. Throughout the 20th century, research interest in nocturnal respiration occurred alongside initial discoveries of CAM, although the energetic and mechanistic implications of nocturnal oxygen consumption and links to the operation of the CAM cycle were not fully understood. Recent flux balance analysis (FBA) models have provided new insights into the role that mitochondria play in the CAM cycle. Several FBA models have predicted that CAM requires elevated nocturnal respiratory rates, compared to C3 species, to power vacuolar malic acid accumulation. We provide physiological data, from the genus Clusia, to corroborate these modelling predictions, thereby reinforcing the importance of elevated nocturnal respiratory rates for CAM. Finally, we outline five unanswered questions pertaining to nocturnal respiration which must be addressed if we are to fully understand and utilize CAM plants in a hotter, drier world.
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Affiliation(s)
- Alistair Leverett
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge CB2 3EA, UK
| | - Anne M Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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4
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Chomthong M, Griffiths H. Prospects and perspectives: inferring physiological and regulatory targets for CAM from molecular and modelling approaches. ANNALS OF BOTANY 2023; 132:583-596. [PMID: 37742290 PMCID: PMC10799989 DOI: 10.1093/aob/mcad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/26/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND AND SCOPE This review summarizes recent advances in our understanding of Crassulacean Acid Metabolism (CAM) by integrating evolutionary, ecological, physiological, metabolic and molecular perspectives. A number of key control loops which moderate the expression of CAM phases, and their metabolic and molecular control, are explored. These include nocturnal stomatal opening, activation of phosphoenolpyruvate carboxylase by a specific protein kinase, interactions with circadian clock control, as well as daytime decarboxylation and activation of Rubisco. The vacuolar storage and release of malic acid and the interplay between the supply and demand for carbohydrate reserves are also key metabolic control points. FUTURE OPPORTUNITIES We identify open questions and opportunities, with experimentation informed by top-down molecular modelling approaches allied with bottom-up mechanistic modelling systems. For example, mining transcriptomic datasets using high-speed systems approaches will help to identify targets for future genetic manipulation experiments to define the regulation of CAM (whether circadian or metabolic control). We emphasize that inferences arising from computational approaches or advanced nuclear sequencing techniques can identify potential genes and transcription factors as regulatory targets. However, these outputs then require systematic evaluation, using genetic manipulation in key model organisms over a developmental progression, combining gene silencing and metabolic flux analysis and modelling to define functionality across the CAM day-night cycle. From an evolutionary perspective, the origins and function of CAM succulents and responses to water deficits are set against the mesophyll and hydraulic limitations imposed by cell and tissue succulence in contrasting morphological lineages. We highlight the interplay between traits across shoots (3D vein density, mesophyll conductance and cell shrinkage) and roots (xylem embolism and segmentation). Thus, molecular, biophysical and biochemical processes help to curtail water losses and exploit rapid rehydration during restorative rain events. In the face of a changing climate, we hope such approaches will stimulate opportunities for future research.
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Affiliation(s)
- Methawi Chomthong
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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Mok D, Leung A, Searles P, Sage TL, Sage RF. CAM photosynthesis in Bulnesia retama (Zygophyllaceae), a non-succulent desert shrub from South America. ANNALS OF BOTANY 2023; 132:655-670. [PMID: 37625031 PMCID: PMC10799978 DOI: 10.1093/aob/mcad114] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/19/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND AND AIMS Bulnesia retama is a drought-deciduous, xerophytic shrub from arid landscapes of South America. In a survey of carbon isotope ratios (δ13C) in specimens from the field, B. retama exhibited less negative values, indicative of CAM or C4 photosynthesis. Here, we investigate whether B. retama is a C4 or CAM plant. METHODS Gas-exchange responses to intercellular CO2, diurnal gas-exchange profiles, δ13C and dawn vs. afternoon titratable acidity were measured on leaves and stems of watered and droughted B. retama plants. Leaf and stem cross-sections were imaged to determine whether the tissues exhibited succulent CAM or C4 Kranz anatomy. KEY RESULTS Field-collected stems and fruits of B. retama exhibited δ13C between -16 and -19 ‰. Plants grown in a glasshouse from field-collected seeds had leaf δ13C values near -31 ‰ and stem δ13C values near -28 ‰. The CO2 response of photosynthesis showed that leaves and stems used C3 photosynthesis during the day, while curvature in the nocturnal response of net CO2 assimilation rate (A) in all stems, coupled with slightly positive rates of A at night, indicated modest CAM function. C4 photosynthesis was absent. Succulence was absent in all tissues, although stems exhibited tight packing of the cortical chlorenchyma in a CAM-like manner. Tissue titratable acidity increased at night in droughted stems. CONCLUSIONS Bulnesia retama is a weak to modest C3 + CAM plant. This is the first report of CAM in the Zygophyllaceae and the first showing that non-succulent, xerophytic shrubs use CAM. CAM alone in B. retama was too limited to explain less negative δ13C in field-collected plants, but combined with effects of low stomatal and mesophyll conductance it could raise δ13C to observed values between -16 and -19 ‰. Modest CAM activity, particularly during severe drought, could enable B. retama to persist in arid habitats of South America.
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Affiliation(s)
- Daniel Mok
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Wilcocks Street, Toronto, Ontario M5R3C6, Canada
| | - Arthur Leung
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Wilcocks Street, Toronto, Ontario M5R3C6, Canada
| | - Peter Searles
- Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja (CRILAR-CONICET), Entre Ríos y Mendoza s/n, Anillaco (5301), La Rioja, Argentina
| | - Tammy L Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Wilcocks Street, Toronto, Ontario M5R3C6, Canada
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Wilcocks Street, Toronto, Ontario M5R3C6, Canada
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6
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Fan W, He ZS, Zhe M, Feng JQ, Zhang L, Huang Y, Liu F, Huang JL, Ya JD, Zhang SB, Yang JB, Zhu A, Li DZ. High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes. PLANT COMMUNICATIONS 2023; 4:100564. [PMID: 36809882 PMCID: PMC10504564 DOI: 10.1016/j.xplc.2023.100564] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Epiphytes with crassulacean acid metabolism (CAM) photosynthesis are widespread among vascular plants, and repeated evolution of CAM photosynthesis is a key innovation for micro-ecosystem adaptation. However, we lack a complete understanding of the molecular regulation of CAM photosynthesis in epiphytes. Here, we report a high-quality chromosome-level genome assembly of a CAM epiphyte, Cymbidium mannii (Orchidaceae). The 2.88-Gb orchid genome with a contig N50 of 22.7 Mb and 27 192 annotated genes was organized into 20 pseudochromosomes, 82.8% of which consisted of repetitive elements. Recent expansions of long terminal repeat retrotransposon families have made a major contribution to the evolution of genome size in Cymbidium orchids. We reveal a holistic scenario of molecular regulation of metabolic physiology using high-resolution transcriptomics, proteomics, and metabolomics data collected across a CAM diel cycle. Patterns of rhythmically oscillating metabolites, especially CAM-related products, reveal circadian rhythmicity in metabolite accumulation in epiphytes. Genome-wide analysis of transcript and protein level regulation revealed phase shifts during the multifaceted regulation of circadian metabolism. Notably, we observed diurnal expression of several core CAM genes (especially βCA and PPC) that may be involved in temporal fixation of carbon sources. Our study provides a valuable resource for investigating post-transcription and translation scenarios in C. mannii, an Orchidaceae model for understanding the evolution of innovative traits in epiphytes.
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Affiliation(s)
- Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zheng-Shan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Mengqing Zhe
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jing-Qiu Feng
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yiwei Huang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | | | - Ji-Dong Ya
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Shi-Bao Zhang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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7
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Tan B, Chen S. Defining Mechanisms of C 3 to CAM Photosynthesis Transition toward Enhancing Crop Stress Resilience. Int J Mol Sci 2023; 24:13072. [PMID: 37685878 PMCID: PMC10487458 DOI: 10.3390/ijms241713072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
Global climate change and population growth are persistently posing threats to natural resources (e.g., freshwater) and agricultural production. Crassulacean acid metabolism (CAM) evolved from C3 photosynthesis as an adaptive form of photosynthesis in hot and arid regions. It features the nocturnal opening of stomata for CO2 assimilation, diurnal closure of stomata for water conservation, and high water-use efficiency. To cope with global climate challenges, the CAM mechanism has attracted renewed attention. Facultative CAM is a specialized form of CAM that normally employs C3 or C4 photosynthesis but can shift to CAM under stress conditions. It not only serves as a model for studying the molecular mechanisms underlying the CAM evolution, but also provides a plausible solution for creating stress-resilient crops with facultative CAM traits. This review mainly discusses the recent research effort in defining the C3 to CAM transition of facultative CAM plants, and highlights challenges and future directions in this important research area with great application potential.
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Affiliation(s)
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA;
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8
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Heyduk K, McAssey EV, Leebens‐Mack J. Differential timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae). THE NEW PHYTOLOGIST 2022; 235:2111-2126. [PMID: 35596719 PMCID: PMC9796715 DOI: 10.1111/nph.18267] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Crassulacean acid metabolism (CAM) photosynthesis has evolved repeatedly across the plant tree of life, however our understanding of the genetic convergence across independent origins remains hampered by the lack of comparative studies. Here, we explore gene expression profiles in eight species from the Agavoideae (Asparagaceae) encompassing three independent origins of CAM. Using comparative physiology and transcriptomics, we examined the variable modes of CAM in this subfamily and the changes in gene expression across time of day and between well watered and drought-stressed treatments. We further assessed gene expression and the molecular evolution of genes encoding phosphoenolpyruvate carboxylase (PPC), an enzyme required for primary carbon fixation in CAM. Most time-of-day expression profiles are largely conserved across all eight species and suggest that large perturbations to the central clock are not required for CAM evolution. By contrast, transcriptional response to drought is highly lineage specific. Yucca and Beschorneria have CAM-like expression of PPC2, a copy of PPC that has never been shown to be recruited for CAM in angiosperms. Together the physiological and transcriptomic comparison of closely related C3 and CAM species reveals similar gene expression profiles, with the notable exception of differential recruitment of carboxylase enzymes for CAM function.
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Affiliation(s)
- Karolina Heyduk
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHI96822USA
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
| | - Edward V. McAssey
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHI96822USA
| | - Jim Leebens‐Mack
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
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9
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Heyduk K. Evolution of Crassulacean acid metabolism in response to the environment: past, present, and future. PLANT PHYSIOLOGY 2022; 190:19-30. [PMID: 35748752 PMCID: PMC9434201 DOI: 10.1093/plphys/kiac303] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Crassulacean acid metabolism (CAM) is a mode of photosynthesis that evolved in response to decreasing CO2 levels in the atmosphere some 20 million years ago. An elevated ratio of O2 relative to CO2 caused many plants to face increasing stress from photorespiration, a process exacerbated for plants living under high temperatures or in water-limited environments. Today, our climate is again rapidly changing and plants' ability to cope with and adapt to these novel environments is critical for their success. This review focuses on CAM plant responses to abiotic stressors likely to dominate in our changing climate: increasing CO2 levels, increasing temperatures, and greater variability in drought. Empirical studies that have assessed CAM responses are reviewed, though notably these are concentrated in relatively few CAM lineages. Other aspects of CAM biology, including the effects of abiotic stress on the light reactions and the role of leaf succulence, are also considered in the context of climate change. Finally, more recent studies using genomic techniques are discussed to link physiological changes in CAM plants with the underlying molecular mechanism. Together, the body of work reviewed suggests that CAM plants will continue to thrive in certain environments under elevated CO2. However, how CO2 interacts with other environmental factors, how those interactions affect CAM plants, and whether all CAM plants will be equally affected remain outstanding questions regarding the evolution of CAM on a changing planet.
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10
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Wong DCJ, Peakall R. Orchid Phylotranscriptomics: The Prospects of Repurposing Multi-Tissue Transcriptomes for Phylogenetic Analysis and Beyond. FRONTIERS IN PLANT SCIENCE 2022; 13:910362. [PMID: 35712597 PMCID: PMC9196242 DOI: 10.3389/fpls.2022.910362] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/21/2022] [Indexed: 06/10/2023]
Abstract
The Orchidaceae is rivaled only by the Asteraceae as the largest plant family, with the estimated number of species exceeding 25,000 and encompassing more than 700 genera. To gain insights into the mechanisms driving species diversity across both global and local scales, well-supported phylogenies targeting different taxonomic groups and/or geographical regions will be crucial. High-throughput sequencing technologies have revolutionized the field of molecular phylogenetics by simplifying the process of obtaining genome-scale sequence data. Consequently, there has been an explosive growth of such data in public repositories. Here we took advantage of this unprecedented access to transcriptome data from predominantly non-phylogenetic studies to assess if it can be repurposed to gain rapid and accurate phylogenetic insights across the orchids. Exhaustive searches revealed transcriptomic data for more than 100 orchid species spanning 5 subfamilies, 13 tribes, 21 subtribes, and 50 genera that were amendable for exploratory phylotranscriptomic analysis. Next, we performed re-assembly of the transcriptomes before strategic selection of the final samples based on a gene completeness evaluation. Drawing on these data, we report phylogenetic analyses at both deep and shallow evolutionary scales via maximum likelihood and shortcut coalescent species tree methods. In this perspective, we discuss some key outcomes of this study and conclude by highlighting other complementary, albeit rarely explored, insights beyond phylogenetic analysis that repurposed multi-tissue transcriptome can offer.
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11
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Yan X, Chang Y, Zhao W, Qian C, Yin X, Fan X, Zhu X, Zhao X, Ma XF. Transcriptome profiling reveals that foliar water uptake occurs with C 3 and crassulacean acid metabolism facultative photosynthesis in Tamarix ramosissima under extreme drought. AOB PLANTS 2022; 14:plab060. [PMID: 35047161 PMCID: PMC8763614 DOI: 10.1093/aobpla/plab060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/14/2022] [Indexed: 05/21/2023]
Abstract
Tamarix ramosissima is a typical desert plant species that is widely distributed in the desert areas of Northwest China. It plays a significant role in sand fixation and soil water conservation. In particular, how it uses water to survive in the desert plays an important role in plant growth and ecosystem function. Previous studies have revealed that T. ramosissima can alleviate drought by absorbing water from its leaves under extreme drought conditions. To date, there is no clear molecular regulation mechanism to explain foliar water uptake (FWU). In the present study, we correlated diurnal meteorological data, sap flow and photosynthetic parameters to determine the physical and biological characteristics of FWU. Our results suggested that the lesser the groundwater, the easier it is for T. ramosissima to absorb water via the leaves. Gene ontology annotation and Kyoto Encyclopaedia of Genes and Genomes pathway analysis of the transcriptome profile of plants subjected to high humidity suggested that FWU was highly correlated to carbohydrate metabolism, energy transfer, pyruvate metabolism, hormone signal transduction and plant-pathogen interaction. Interestingly, as a C3 plant, genes such as PEPC, PPDK, MDH and RuBP, which are involved in crassulacean acid metabolism (CAM) photosynthesis, were highly upregulated and accompanied by FWU. Therefore, we proposed that in the case of sufficient water supply, C3 photosynthesis is used in T. ramosissima, whereas in cases of extreme drought, starch is degraded to provide CO2 for CAM photosynthesis to make full use of the water obtained via FWU and the water that was transported or stored to assimilating branches and stems. This study may provide not only an important theoretical foundation for FWU and conversion from C3 plants to CAM plants but also for engineering improved photosynthesis in high-yield drought-tolerant plants and mitigation of climate change-driven drought.
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Affiliation(s)
- Xia Yan
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, China
- Key Laboratory of Inland River Ecohydrology, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Yan Chang
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, China
| | - Weijia Zhao
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, China
| | - Chaoju Qian
- Key Laboratory of Stress Physiology and Ecology in Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Xiaoyue Yin
- Key Laboratory of Stress Physiology and Ecology in Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingke Fan
- Key Laboratory of Stress Physiology and Ecology in Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyu Zhu
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, China
| | - Xiangqiang Zhao
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, China
| | - Xiao-Fei Ma
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, China
- Key Laboratory of Stress Physiology and Ecology in Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- Corresponding author’s e-mail address:
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12
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Winter K, Smith JAC. CAM photosynthesis: the acid test. THE NEW PHYTOLOGIST 2022; 233:599-609. [PMID: 34637529 PMCID: PMC9298356 DOI: 10.1111/nph.17790] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/27/2021] [Indexed: 05/04/2023]
Abstract
There is currently considerable interest in the prospects for bioengineering crassulacean acid metabolism (CAM) photosynthesis - or key elements associated with it, such as increased water-use efficiency - into C3 plants. Resolving how CAM photosynthesis evolved from the ancestral C3 pathway could provide valuable insights into the targets for such bioengineering efforts. It has been proposed that the ability to accumulate organic acids at night may be common among C3 plants, and that the transition to CAM might simply require enhancement of pre-existing fluxes, without the need for changes in circadian or diurnal regulation. We show, in a survey encompassing 40 families of vascular plants, that nocturnal acidification is a feature entirely restricted to CAM species. Although many C3 species can synthesize malate during the light period, we argue that the switch to night-time malic acid accumulation requires a fundamental metabolic reprogramming that couples glycolytic breakdown of storage carbohydrate to the process of net dark CO2 fixation. This central element of the CAM pathway, even when expressed at a low level, represents a biochemical capability not seen in C3 plants, and so is better regarded as a discrete evolutionary innovation than as part of a metabolic continuum between C3 and CAM.
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Affiliation(s)
- Klaus Winter
- Smithsonian Tropical Research InstitutePO Box 0843‐03092BalboaAncónRepublic of Panama
| | - J. Andrew C. Smith
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
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Abstract
To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigate underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identify several key differences. Notably, Isoetes may have recruited the lesser-known 'bacterial-type' PEPC, along with the 'plant-type' exclusively used in other CAM and C4 plants for carboxylation of PEP. Furthermore, we find that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized.
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Gamisch A, Winter K, Fischer GA, Comes HP. Evolution of crassulacean acid metabolism (CAM) as an escape from ecological niche conservatism in Malagasy Bulbophyllum (Orchidaceae). THE NEW PHYTOLOGIST 2021; 231:1236-1248. [PMID: 33960438 DOI: 10.1111/nph.17437] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/21/2021] [Indexed: 05/29/2023]
Abstract
Despite growing evidence that niche shifts are more common in flowering plants than previously thought, little is known of whether such shifts are promoted by changes in photosynthetic pathways. Here we combine the most complete phylogeny for epiphytic Malagasy Bulbophyllum orchids (c. 210 spp.) with climatic niche and carbon isotope ratios to infer the group's spatial-temporal history, and the role of strongly expressed crassulacean acid metabolism (CAM) in facilitating niche shifts and diversification. We find that most extant species still retain niche (Central Highland) and photosynthesis (C3 ) states as present in the single mid-Miocene (c. 12.70 million yr ago (Ma)) ancestor colonizing Madagascar. However, we also infer a major transition to CAM, linked to a late Miocene (c. 7.36 Ma) invasion of species from the sub-humid highland first into the island's humid eastern coastal, and then into the seasonally dry 'Northwest Sambirano' rainforests, yet without significant effect on diversification rates. These findings indicate that CAM in tropical epiphytes may be selectively advantageous even in high rainfall habitats, rather than presenting a mere adaptation to dry environments or epiphytism per se. Overall, our study qualifies CAM as an evolutionary 'gateway' trait that considerably widened the spatial-ecological amplitude of Madagascar's most species-rich orchid genus.
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Affiliation(s)
- Alexander Gamisch
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, Salzburg, 5020, Austria
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama
| | - Gunter A Fischer
- Kadoorie Farm and Botanic Garden Corporation, Lam Kam Road, Tai Po, NT, Hong Kong SAR, China
| | - Hans Peter Comes
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, Salzburg, 5020, Austria
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You X, Yin S, Suo F, Xu Z, Chu D, Kong Q, Zhang C, Li Y, Liu L. Biochar and fertilizer improved the growth and quality of the ice plant (Mesembryanthemum crystallinum L.) shoots in a coastal soil of Yellow River Delta, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 775:144893. [PMID: 33618299 DOI: 10.1016/j.scitotenv.2020.144893] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Coastal soil is an important land reserve that may be used to alleviate the shortage of cultivated land; however, this soil is stressed by saline conditions and nutrient deficiency. Biochar offers the potential to reclaim coastal soil, but the response of plant growth to biochar addition in salt-affected soil is species-dependent. In this study, the response of ice plant (Mesembryanthemum crystallinum L.), an economically valuable halophyte that grows in the coastal soil of the Yellow River Delta, to wood chip biochar (WBC) either alone or in combination with chemical fertilizer was investigated using a 90-day pot experiment. The WBC enhanced the growth of ice plants in the coastal soil, but combining it with chemical fertilizer did not increase its effect. The nutritional quality of the plants was improved by the addition of WBC, regardless of whether chemical fertilizer was applied; moreover, WBC amendment enhanced photosynthesis and reduced the oxidative stress of the plants. The ameliorated soil properties (e.g., soil organic matter and water holding capacity) and increased contents of available macronutrients (e.g., P and K) and micronutrients (e.g., Mg, Mn, B and Zn) resulting from soil amendment with WBC may have contributed to the enhanced growth and quality of the ice plants. Additionally, in soil modified with WBC, an increased abundance of beneficial taxa (e.g., Erythrobacter, Sphingomonas and Lysobacter) and a shift in the microbial community may also have helped to improve the growth and quality of the ice plants. The results of our study provide useful information for developing a biochar-based technology to use in combination with valuable halophytes to reclaim degraded coastal soil and enhance food security.
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Affiliation(s)
- Xiangwei You
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Shaojing Yin
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Fengyue Suo
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zongchang Xu
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Depeng Chu
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Qingxian Kong
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Chengsheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Lei Liu
- Qingdao Bureau of Agriculture and Rural Affairs, Qingdao 266100, China
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Winter K, Virgo A, Garcia M, Aranda J, Holtum JAM. Constitutive and facultative crassulacean acid metabolism (CAM) in Cuban oregano, Coleus amboinicus (Lamiaceae). FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:647-654. [PMID: 32919492 DOI: 10.1071/fp20127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Plants exhibiting the water-conserving crassulacean acid metabolism (CAM) photosynthetic pathway provide some of the most intriguing examples of photosynthetic diversity and plasticity. Here, a largely unnoticed facet of CAM-plant photosynthesis is highlighted: the co-occurrence of ontogenetically controlled constitutive and environmentally controlled facultative CAM in a species. Both forms of CAM are displayed in leaves of Coleus amboinicus Lour. (Lamiaceae), a semi-succulent perennial plant with oregano-like flavour that is native to southern and eastern Africa and naturalised elsewhere in the tropics. Under well-watered conditions, leaves assimilate CO2 predominantly by the C3 pathway. They also display low levels of CO2 uptake at night accompanied by small nocturnal increases in leaf tissue acidity. This indicates the presence of weakly expressed constitutive CAM. CAM expression is strongly enhanced in response to drought stress. The drought-enhanced component of CAM is reversible upon rewatering and thus considered to be facultative. In contrast to C. amboinicus, the thin-leaved closely related Coleus scutellarioides (L.) Benth. exhibits net CO2 fixation solely in the light via the C3 pathway, both under well-watered and drought conditions. However, low levels of nocturnal acidification detected in leaves and stems indicate that the CAM cycle is present. The highly speciose mint family, which contains few known CAM-exhibiting species and is composed predominantly of C3 species, appears to be an excellent group of plants for studying the evolutionary origins of CAM and for determining the position of facultative CAM along the C3-full CAM trajectory.
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Affiliation(s)
- Klaus Winter
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama; and Corresponding author.
| | - Aurelio Virgo
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama
| | - Milton Garcia
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama
| | - Jorge Aranda
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama
| | - Joseph A M Holtum
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama; and College of Science and Engineering, James Cook University, Townsville, Qld 4811, Australia
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Boxall SF, Kadu N, Dever LV, Kneřová J, Waller JL, Gould PJD, Hartwell J. Kalanchoë PPC1 Is Essential for Crassulacean Acid Metabolism and the Regulation of Core Circadian Clock and Guard Cell Signaling Genes. THE PLANT CELL 2020; 32:1136-1160. [PMID: 32051209 PMCID: PMC7145507 DOI: 10.1105/tpc.19.00481] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 01/28/2020] [Accepted: 02/09/2020] [Indexed: 05/21/2023]
Abstract
Unlike C3 plants, Crassulacean acid metabolism (CAM) plants fix CO2 in the dark using phosphoenolpyruvate carboxylase (PPC; EC 4.1.1.31). PPC combines phosphoenolpyruvate with CO2 (as HCO3 -), forming oxaloacetate. The oxaloacetate is converted to malate, leading to malic acid accumulation in the vacuole, which peaks at dawn. During the light period, malate decarboxylation concentrates CO2 around Rubisco for secondary fixation. CAM mutants lacking PPC have not been described. Here, we employed RNA interference to silence the CAM isogene PPC1 in Kalanchoë laxiflora Line rPPC1-B lacked PPC1 transcripts, PPC activity, dark period CO2 fixation, and nocturnal malate accumulation. Light period stomatal closure was also perturbed, and the plants displayed reduced but detectable dark period stomatal conductance and arrhythmia of the CAM CO2 fixation circadian rhythm under constant light and temperature free-running conditions. By contrast, the rhythm of delayed fluorescence was enhanced in plants lacking PPC1 Furthermore, a subset of gene transcripts within the central circadian oscillator was upregulated and oscillated robustly in this line. The regulation of guard cell genes involved in controlling stomatal movements was also perturbed in rPPC1-B These findings provide direct evidence that the regulatory patterns of key guard cell signaling genes are linked with the characteristic inverse pattern of stomatal opening and closing during CAM.
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Affiliation(s)
- Susanna F Boxall
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Nirja Kadu
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Louisa V Dever
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Jana Kneřová
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Jade L Waller
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Peter J D Gould
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - James Hartwell
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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18
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Chen LY, Xin Y, Wai CM, Liu J, Ming R. The role of cis-elements in the evolution of crassulacean acid metabolism photosynthesis. HORTICULTURE RESEARCH 2020; 7:5. [PMID: 31908808 PMCID: PMC6938490 DOI: 10.1038/s41438-019-0229-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/01/2019] [Accepted: 12/04/2019] [Indexed: 05/30/2023]
Abstract
Crassulacean acid metabolism (CAM) photosynthesis is an innovation of carbon concentrating mechanism that is characterized by nocturnal CO2 fixation. Recent progresses in genomics, transcriptomics, proteomics, and metabolomics of CAM species yielded new knowledge and abundant genomic resources. In this review, we will discuss the pattern of cis-elements in stomata movement-related genes and CAM CO2 fixation genes, and analyze the expression dynamic of CAM related genes in green leaf tissues. We propose that CAM photosynthesis evolved through the re-organization of existing enzymes and associated membrane transporters in central metabolism and stomatal movement-related genes, at least in part by selection of existing circadian clock cis-regulatory elements in their promoter regions. Better understanding of CAM evolution will help us to design crops that can thrive in arid or semi-arid regions, which are likely to expand due to global climate change.
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Affiliation(s)
- Li-Yu Chen
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Yinghui Xin
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Juan Liu
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Ray Ming
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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Yang X, Liu D, Tschaplinski TJ, Tuskan GA. Comparative genomics can provide new insights into the evolutionary mechanisms and gene function in CAM plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6539-6547. [PMID: 31616946 PMCID: PMC6883262 DOI: 10.1093/jxb/erz408] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/29/2019] [Indexed: 05/24/2023]
Abstract
Crassulacean acid metabolism (CAM) photosynthesis is an important biological innovation enabling plant adaptation to hot and dry environments. CAM plants feature high water-use efficiency, with potential for sustainable crop production under water-limited conditions. A deep understanding of CAM-related gene function and molecular evolution of CAM plants is critical for exploiting the potential of engineering CAM into C3 crops to enhance crop production on semi-arid or marginal agricultural lands. With the newly emerging genomics resources for multiple CAM species, progress has been made in comparative genomics studies on the molecular basis and subsequently on the evolution of CAM. Here, recent advances in CAM comparative genomics research in constitutive and facultative CAM plants are reviewed, with a focus on the analyses of DNA/protein sequences and gene expression to provide new insights into the path and driving force of CAM evolution and to identify candidate genes involved in CAM-related biological processes. Potential applications of new computational and experimental technologies (e.g. CRISPR/Cas-mediated genome-editing technology) to the comparative and evolutionary genomics research on CAM plants are offered.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, USA
| | - Degao Liu
- Department of Genetics, Cell Biology and Development and Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, USA
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Davis SC, Simpson J, Gil-Vega KDC, Niechayev NA, van Tongerlo E, Castano NH, Dever LV, Búrquez A. Undervalued potential of crassulacean acid metabolism for current and future agricultural production. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6521-6537. [PMID: 31087091 PMCID: PMC6883259 DOI: 10.1093/jxb/erz223] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/03/2019] [Indexed: 05/11/2023]
Abstract
The potential for crassulacean acid metabolism (CAM) to support resilient crops that meet demands for food, fiber, fuel, and pharmaceutical products far exceeds current production levels. This review provides background on five families of plants that express CAM, including examples of many species within these families that have potential agricultural uses. We summarize traditional uses, current developments, management practices, environmental tolerance ranges, and economic values of CAM species with potential commercial applications. The primary benefit of CAM in agriculture is high water use efficiency that allows for reliable crop yields even in drought conditions. Agave species, for example, grow in arid conditions and have been exploited for agricultural products in North and South America for centuries. Yet, there has been very little investment in agricultural improvement for most useful Agave varieties. Other CAM species that are already traded globally include Ananas comosus (pineapple), Aloe spp., Vanilla spp., and Opuntia spp., but there are far more with agronomic uses that are less well known and not yet developed commercially. Recent advances in technology and genomic resources provide tools to understand and realize the tremendous potential for using CAM crops to produce climate-resilient agricultural commodities in the future.
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Affiliation(s)
- Sarah C Davis
- Voinovich School of Leadership and Public Affairs, Ohio University, Athens, OH, USA
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, USA
| | - June Simpson
- Department of Genetic Engineering, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, México
| | | | - Nicholas A Niechayev
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Evelien van Tongerlo
- Horticulture and Product Physiology, Wageningen University, Wageningen, The Netherlands
| | | | - Louisa V Dever
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Alberto Búrquez
- Instituto de Ecología, Universidad Nacional Autónoma de México, Unidad Hermosillo, Sonora, México
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21
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Li MH, Liu DK, Zhang GQ, Deng H, Tu XD, Wang Y, Lan SR, Liu ZJ. A perspective on crassulacean acid metabolism photosynthesis evolution of orchids on different continents: Dendrobium as a case study. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6611-6619. [PMID: 31625570 DOI: 10.1093/jxb/erz461] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 10/05/2019] [Indexed: 05/26/2023]
Abstract
Members of the Orchidaceae, one of the largest families of flowering plants, evolved the crassulacean acid metabolism (CAM) photosynthesis strategy. It is thought that CAM triggers adaptive radiation into new niche spaces, yet very little is known about its origin and diversification on different continents. Here, we assess the prevalence of CAM in Dendrobium, which is one of the largest genera of flowering plants and found in a wide range of environments, from the high altitudes of the Himalayas to relatively arid habitats in Australia. Based on phylogenetic time trees, we estimated that CAM, as determined by δ 13C values less negative than -20.0‰, evolved independently at least eight times in Dendrobium. The oldest lineage appeared in the Asian clade during the middle Miocene, indicating the origin of CAM was associated with a pronounced climatic cooling that followed a period of aridity. Divergence of the four CAM lineages in the Asian clade appeared to be earlier than divergence of those in the Australasian clade. However, CAM species in the Asian clade are much less diverse (25.6%) than those in the Australasian clade (57.9%). These findings shed new light on CAM evolutionary history and the aridity levels of the paleoclimate on different continents.
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Affiliation(s)
- Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Hua Deng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiong-De Tu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Si-Ren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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