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Siadjeu C, Kadereit G. C 4-like Sesuvium sesuvioides (Aizoaceae) exhibits CAM in cotyledons and putative C 4-like + CAM metabolism in adult leaves as revealed by transcriptome analysis. BMC Genomics 2024; 25:688. [PMID: 39003461 PMCID: PMC11245778 DOI: 10.1186/s12864-024-10553-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 06/21/2024] [Indexed: 07/15/2024] Open
Abstract
BACKGROUND The co-occurrence of C4 and CAM photosynthesis in a single species seems to be unusual and rare. This is likely due to the difficulty in effectively co-regulating both pathways. Here, we conducted a comparative transcriptomic analysis of leaves and cotyledons of the C4-like species Sesuvium sesuvioides (Aizoaceae) using RNA-seq. RESULTS When compared to cotyledons, phosphoenolpyruvate carboxylase 4 (PEPC4) and some key C4 genes were found to be up-regulated in leaves. During the day, the expression of NADP-dependent malic enzyme (NADP-ME) was significantly higher in cotyledons than in leaves. The titratable acidity confirmed higher acidity in the morning than in the previous evening indicating the induction of weak CAM in cotyledons by environmental conditions. Comparison of the leaves of S. sesuvioides (C4-like) and S. portulacastrum (C3) revealed that PEPC1 was significantly higher in S. sesuvioides, while PEPC3 and PEPC4 were up-regulated in S. portulacastrum. Finally, potential key regulatory elements involved in the C4-like and CAM pathways were identified. CONCLUSIONS These findings provide a new species in which C4-like and CAM co-occur and raise the question if this phenomenon is indeed so rare or just hard to detect and probably more common in succulent C4 lineages.
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Affiliation(s)
- Christian Siadjeu
- Prinzessin Therese von Bayern Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilans-Universität München, Menzinger Str. 67, Munich, 80638, Germany.
| | - Gudrun Kadereit
- Prinzessin Therese von Bayern Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilans-Universität München, Menzinger Str. 67, Munich, 80638, Germany
- Botanischer Garten München-Nymphenburg Und Botanische Staatssammlung München, Staatliche Naturwissenschaftliche Sammlungen Bayerns, Menzinger Str. 65, Munich, 80638, Germany
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2
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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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3
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Ludwig M, Hartwell J, Raines CA, Simkin AJ. The Calvin-Benson-Bassham cycle in C 4 and Crassulacean acid metabolism species. Semin Cell Dev Biol 2024; 155:10-22. [PMID: 37544777 DOI: 10.1016/j.semcdb.2023.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/03/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023]
Abstract
The Calvin-Benson-Bassham (CBB) cycle is the ancestral CO2 assimilation pathway and is found in all photosynthetic organisms. Biochemical extensions to the CBB cycle have evolved that allow the resulting pathways to act as CO2 concentrating mechanisms, either spatially in the case of C4 photosynthesis or temporally in the case of Crassulacean acid metabolism (CAM). While the biochemical steps in the C4 and CAM pathways are known, questions remain on their integration and regulation with CBB cycle activity. The application of omic and transgenic technologies is providing a more complete understanding of the biochemistry of C4 and CAM species and will also provide insight into the CBB cycle in these plants. As the global population increases, new solutions are required to increase crop yields and meet demands for food and other bioproducts. Previous work in C3 species has shown that increasing carbon assimilation through genetic manipulation of the CBB cycle can increase biomass and yield. There may also be options to improve photosynthesis in species using C4 photosynthesis and CAM through manipulation of the CBB cycle in these plants. This is an underexplored strategy and requires more basic knowledge of CBB cycle operation in these species to enable approaches for increased productivity.
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Affiliation(s)
- Martha Ludwig
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | | | - Andrew J Simkin
- University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK; School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
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4
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Winter K, Holtum JAM. Shifting photosynthesis between the fast and slow lane: Facultative CAM and water-deficit stress. JOURNAL OF PLANT PHYSIOLOGY 2024; 294:154185. [PMID: 38373389 DOI: 10.1016/j.jplph.2024.154185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/28/2023] [Accepted: 01/20/2024] [Indexed: 02/21/2024]
Abstract
Five decades ago, the first report of a shift from C3 to CAM (crassulacean acid metabolism) photosynthesis following the imposition of stress was published in this journal. The annual, Mesembryanthemum crystallinum (Aizoaceae), was shown to be a C3 plant when grown under non-saline conditions, and a CAM plant when exposed to high soil salinity. This observation of environmentally triggered CAM eventually led to the introduction of the term facultative CAM, which categorises CAM that is induced or upregulated in response to water-deficit stress and is lost or downregulated when the stress is removed. Reversibility of C3-to-CAM shifts distinguishes stress-driven facultative-CAM responses from purely ontogenetic increases of CAM activity. We briefly review how the understanding of facultative CAM has developed, evaluate the current state of knowledge, and highlight questions of continuing interest. We demonstrate that the long-lived leaves of a perennial facultative-CAM arborescent species, Clusia pratensis, can repeatedly switch between C3 and CAM in response to multiple wet-dry-wet cycles. Undoubtedly, this is a dedicated response to environment, independent of ontogeny. We highlight the potential for engineering facultative CAM into C3 crops to provide a flexible capacity for drought tolerance.
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Affiliation(s)
- Klaus Winter
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Panama City, Panama.
| | - Joseph A M Holtum
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
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5
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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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6
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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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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: 4] [Impact Index Per Article: 4.0] [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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Ferrari RC, Kawabata AB, Ferreira SS, Hartwell J, Freschi L. A matter of time: regulatory events behind the synchronization of C4 and crassulacean acid metabolism in Portulaca oleracea. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4867-4885. [PMID: 35439821 DOI: 10.1093/jxb/erac163] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Portulaca species can switch between C4 and crassulacean acid metabolism (CAM) depending on environmental conditions. However, the regulatory mechanisms behind this rare photosynthetic adaptation remain elusive. Using Portulaca oleracea as a model system, here we investigated the involvement of the circadian clock, plant hormones, and transcription factors in coordinating C4 and CAM gene expression. Free-running experiments in constant conditions suggested that C4 and CAM gene expression are intrinsically connected to the circadian clock. Detailed time-course, drought, and rewatering experiments revealed distinct time frames for CAM induction and reversion (days versus hours, respectively), which were accompanied by changes in abscisic acid (ABA) and cytokinin metabolism and signaling. Exogenous ABA and cytokinins were shown to promote and repress CAM expression in P. oleracea, respectively. Moreover, the drought-induced decline in C4 transcript levels was completely recovered upon cytokinin treatment. The ABA-regulated transcription factor genes HB7, NFYA7, NFYC9, TT8, and ARR12 were identified as likely candidate regulators of CAM induction following this approach, whereas NFYC4 and ARR9 were connected to C4 expression patterns. Therefore, we provide insights into the signaling events controlling C4-CAM transitions in response to water availability and over the day/night cycle, highlighting candidate genes for future functional studies in the context of facultative C4-CAM photosynthesis.
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Affiliation(s)
- Renata Callegari Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Aline Bastos Kawabata
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Sávio Siqueira Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
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9
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Aguilar-Benitez D, Casimiro-Soriguer I, Ferrandiz C, Torres AM. Study and QTL mapping of reproductive and morphological traits implicated in the autofertility of faba bean. BMC PLANT BIOLOGY 2022; 22:175. [PMID: 35387612 PMCID: PMC8985305 DOI: 10.1186/s12870-022-03499-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Autofertility describes the ability of faba bean flowers to self-fertilize thereby ensuring the productivity of this crop in the absence of pollinators or mechanical disturbance. In the legume crop faba bean (Vicia faba L.), lack of autofertility in a context of insufficient pollination can lead to a severe decrease in grain yield. Here we performed the first QTL analysis aimed at identifying the genomic regions controlling autofertility in this crop. We combined pod and seed setting scores from a recombinant inbred population (RIL) segregating for autofertility in different environments and years with measurements of morphological floral traits and pollen production and viability. This approach revealed 19 QTLs co-localizing in six genomic regions. Extensive co-localization was evident for various floral features whose QTLs clustered in chrs. I, II and V, while other QTLs in chrs. III, IV and VI revealed co-localization of flower characteristics and pod and seed set data. The percentage of phenotypic variation explained by the QTLs ranged from 8.9 for style length to 25.7 for stigma angle. In the three QTLs explaining the highest phenotypic variation (R 2 > 20), the marker alleles derived from the autofertile line Vf27. We further inspected positional candidates identified by these QTLs which represent a valuable resource for further validation. Our results advance the understanding of autofertility in faba bean and will aid the identification of responsible genes for genomic-assisted breeding in this crop.
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Affiliation(s)
- David Aguilar-Benitez
- Área de Mejora y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo. 3092, 14080, Córdoba, Spain
| | - Inés Casimiro-Soriguer
- Área de Mejora y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo. 3092, 14080, Córdoba, Spain.
| | - Cristina Ferrandiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politécnica de Valencia, 46022, Valencia, Spain
| | - Ana M Torres
- Área de Mejora y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo. 3092, 14080, Córdoba, Spain
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10
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Abstract
Crassulacean acid metabolism (CAM) has evolved from a C3 ground state to increase water use efficiency of photosynthesis. During CAM evolution, selective pressures altered the abundance and expression patterns of C3 genes and their regulators to enable the trait. The circadian pattern of CO2 fixation and the stomatal opening pattern observed in CAM can be explained largely with a regulatory architecture already present in C3 plants. The metabolic CAM cycle relies on enzymes and transporters that exist in C3 plants and requires tight regulatory control to avoid futile cycles between carboxylation and decarboxylation. Ecological observations and modeling point to mesophyll conductance as a major factor during CAM evolution. The present state of knowledge enables suggestions for genes for a minimal CAM cycle for proof-of-concept engineering, assuming altered regulation of starch synthesis and degradation are not critical elements of CAM photosynthesis and sufficient malic acid export from the vacuole is possible.
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Affiliation(s)
- Katharina Schiller
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
| | - Andrea Bräutigam
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
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11
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Mayer JA, Wone BWM, Alexander DC, Guo L, Ryals JA, Cushman JC. Metabolic profiling of epidermal and mesophyll tissues under water-deficit stress in Opuntia ficus-indica reveals stress-adaptive metabolic responses. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:717-731. [PMID: 33896444 DOI: 10.1071/fp20332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Cactus pear (Opuntia ficus-indica) is a high productivity species within the Cactaceae grown in many semiarid parts of the world for food, fodder, forage, and biofuels. O. ficus-indica utilises obligate crassulacean acid metabolism (CAM), an adaptation that greatly improves water-use efficiency (WUE) and reduces crop water usage. To better understand CAM-related metabolites and water-deficit stress responses of O. ficus-indica, comparative metabolic profiling was performed on mesophyll and epidermal tissues collected from well-watered and water-deficit stressed cladodes at 50% relative water content (RWC). Tissues were collected over a 24-h period to identify metabolite levels throughout the diel cycle and analysed using a combination of acidic/basic ultra-high-performance liquid chromatography/tandem mass spectrometry (UHPLC/MS/MS) and gas chromatography/mass spectrometry (GC/MS) platforms. A total of 382 metabolites, including 210 (55%) named and 172 (45%) unnamed compounds, were characterised across both tissues. Most tricarboxylic acid (TCA) cycle and glycolysis intermediates were depleted in plants undergoing water-deficit stress indicative of CAM idling or post-idling, while the raffinose family oligosaccharides (RFO) accumulated in both mesophyll and epidermal tissues as osmoprotectants. Levels of reduced glutathione and other metabolites of the ascorbate cycle as well as oxylipins, stress hormones such as traumatic acid, and nucleotide degradation products were increased under water-deficit stress conditions. Notably, tryptophan accumulation, an atypical response, was significantly (24-fold) higher during all time points in water-deficit stressed mesophyll tissue compared with well-watered controls. Many of the metabolite increases were indicative of a highly oxidising environment under water-deficit stress. A total of 34 unnamed metabolites also accumulated in response to water-deficit stress indicating that such compounds might play important roles in water-deficit stress tolerance.
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Affiliation(s)
- Jesse A Mayer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA; and Present address: Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | - Bernard W M Wone
- Department of Biology, University of South Dakota, SD 57069, USA
| | | | - Lining Guo
- Metabolon Inc., 800 Capitola Drive, Suite 1, Durham, NC 27713, USA
| | - John A Ryals
- Metabolon Inc., 800 Capitola Drive, Suite 1, Durham, NC 27713, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA; and Corresponding author.
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12
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Callegari Ferrari R, Pires Bittencourt P, Yumi Nagumo P, Silva Oliveira W, Aurineide Rodrigues M, Hartwell J, Freschi L. Developing Portulaca oleracea as a model system for functional genomics analysis of C 4/CAM photosynthesis. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:666-682. [PMID: 33256895 DOI: 10.1071/fp20202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Previously regarded as an intriguing photosynthetic curiosity, the occurrence of C4 and Crassulacean acid metabolism (CAM) photosynthesis within a single organism has recently emerged as a source of information for future biotechnological use. Among C4/CAM facultative species, Portulaca oleracea L. has been used as a model for biochemical and gene expression analysis of C4/CAM under field and laboratory conditions. In the present work, we focussed on developing molecular tools to facilitate functional genomics studies in this species, from the optimisation of RNA isolation protocols to a method for stable genetic transformation. Eleven variations of RNA extraction procedures were tested and compared for RNA quantity and quality. Also, 7 sample sets comprising total RNA from hormonal and abiotic stress treatments, distinct plant organs, leaf developmental stages, and subspecies were used to select, among 12 reference genes, the most stable reference genes for RT-qPCR analysis of each experimental condition. Furthermore, different explant sources, Agrobacterium tumefaciens strains, and regeneration and antibiotic selection media were tested in various combinations to optimise a protocol for stable genetic transformation of P. oleracea. Altogether, we provide essential tools for functional gene analysis in the context of C4/CAM photosynthesis, including an efficient RNA isolation method, preferred reference genes for RT-qPCR normalisation for a range of experimental conditions, and a protocol to produce P. oleracea stable transformants using A. tumefaciens.
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Affiliation(s)
- Renata Callegari Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Priscila Pires Bittencourt
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Paula Yumi Nagumo
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Willian Silva Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - Maria Aurineide Rodrigues
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brasil; and Corresponding author.
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13
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Ferrari RC, Cruz BC, Gastaldi VD, Storl T, Ferrari EC, Boxall SF, Hartwell J, Freschi L. Exploring C 4-CAM plasticity within the Portulaca oleracea complex. Sci Rep 2020; 10:14237. [PMID: 32859905 PMCID: PMC7455729 DOI: 10.1038/s41598-020-71012-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/29/2020] [Indexed: 11/21/2022] Open
Abstract
Portulaca oleracea is a C4 herb capable of performing CAM under drought stress. It is distributed worldwide and is either considered a polymorphic species or a complex of subspecies, due to its numerous morphological variations. We evaluated CAM plasticity within P. oleracea genotypes since the complexity surrounding this species may be reflected in intraspecific variations in photosynthetic behavior. Eleven subspecies of P. oleracea from distant geographical locations and one cultivar were morphologically and physiologically characterized. C4 and CAM photosynthesis were monitored in plants exposed to well-watered, droughted and rewatered treatments, and data obtained were compared among individual genotypes. All subspecies expressed CAM in a fully-reversible manner. Transcript abundance of C4–CAM signature genes was shown to be a useful indicator of the C4–CAM–C4 switches in all genotypes. C4-related genes were down-regulated and subsequently fully expressed upon drought and rewatering, respectively. CAM-marker genes followed the opposite pattern. A gradient of morphological traits and drought-induced nighttime malate accumulation was observed across genotypes. Therefore, different combinations of CAM expression levels, plant sizes and shapes are available within the P. oleracea complex, which can be a valuable tool in the context of C4/CAM photosynthesis research.
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Affiliation(s)
- Renata Callegari Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Bruna Coelho Cruz
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | | | - Thalyson Storl
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Elisa Callegari Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Susanna F Boxall
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - James Hartwell
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil.
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14
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Chomthong M, Griffiths H. Model approaches to advance crassulacean acid metabolism system integration. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:951-963. [PMID: 31943394 DOI: 10.1111/tpj.14691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
This review summarises recent progress in understanding crassulacean acid metabolism (CAM) systems and the integration of internal and external stimuli to maximise water-use efficiency. Complex CAM traits have been reduced to their minimum and captured as computational models, which can now be refined using recently available data from transgenic manipulations and large-scale omics studies. We identify three key areas in which an appropriate choice of modelling tool could help capture relevant comparative molecular data to address the evolutionary drivers and plasticity of CAM. One focus is to identify the environmental and internal signals that drive inverse stomatal opening at night. Secondly, it is important to identify the regulatory processes required to orchestrate the diel pattern of carbon fluxes within mesophyll layers. Finally, the limitations imposed by contrasting succulent systems and associated hydraulic conductance components should be compared in the context of water-use and evolutionary strategies. While network analysis of transcriptomic data can provide insights via co-expression modules and hubs, alternative forms of computational modelling should be used iteratively to define the physiological significance of key components and informing targeted functional gene manipulation studies. We conclude that the resultant improvements of bottom-up, mechanistic modelling systems can enhance progress towards capturing the physiological controls for phylogenetically diverse CAM systems in the face of the recent surge of information in this omics era.
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Affiliation(s)
- Methawi Chomthong
- Department of Plant Sciences, University of Cambridge, Downing street, Cambridge, CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing street, Cambridge, CB2 3EA, UK
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15
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Hultine KR, Cushman JC, Williams DG. New perspectives on crassulacean acid metabolism biology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6489-6493. [PMID: 31782509 PMCID: PMC6883260 DOI: 10.1093/jxb/erz465] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Kevin R Hultine
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
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16
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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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